Antisense oligomers for the treatment of nonsense-mediated RNA decay-based conditions and diseases

Abstract

To provide a therapeutic agent which can target selective splicing events in a gene and can be used to treat conditions or diseases caused by protein deficiency.SOLUTION: There is provided a method of modulating expression of a target protein by a cell having an mRNA that comprises a non-sense mediated RNA degradation mechanism-inducing exon (NMD exon) and encodes the target protein. The method comprises contacting a therapeutic agent to the cell, by which the therapeutic agent modulates splicing of the NMD exon from the mRNA, thereby modulating a level of processed mRNA encoding the target protein, and modulating expression of the target protein in the cell. The target protein is selected from a group consisting of specific proteins.SELECTED DRAWING: Figure 1B

Description

[Technical Field]

[0001] cross reference

[0001] This application claims the benefit of U.S. Provisional Application No. 62 / 575,924, filed October 23, 2017, and U.S. Provisional Application No. 62 / 667,200, filed May 4, 2018, each of which is incorporated herein by reference in its entirety. [Background technology]

[0002]

[0002] Alternative splicing events in genes can result in non-productive mRNA transcripts that can lead to abnormal protein expression, and therapeutic agents that can target alternative splicing events in genes can regulate the expression level of functional proteins in patients and / or inhibit abnormal protein expression. Such therapeutic agents can be used to treat conditions or diseases caused by protein deficiencies. Summary of the Invention [Means for solving the problem]

[0003] In certain embodiments, a method for modulating expression of a target protein by a cell having an mRNA that includes a nonsense-mediated RNA decay-guided exon (NMD exon) and encodes the target protein comprises contacting the cell with a therapeutic agent, whereby the therapeutic agent modulates splicing of the NMD exon from the mRNA, thereby modulating the level of processed mRNA encoding the target protein and modulating expression of the target protein in the cell, wherein the target protein is selected from the group consisting of AKT3, CACNA1A, CBS, CD46, CFH, CHD2, CLN3, COL11A2, COL4A3, COL4A4, and COL4A. 4, CR1, CRX, CYP2J2, DHDDS, DNAJC8, EIF2AK3, ERN1, GALE, GUCY2F, GUCY2F, HEXA, HEXA, MAPK3, MBD5, MBD5, MBD5, MBD5, MUT, MYH14, MYO6, NF1, NF2, NIPBL, NR1H4, NSD1, NSD1, NSD1, NSD1, OPA1, OPA1, PCCA, PKP2, PPARA, PRPF3, PRPF3, SCN2A, SCN8A, SCN8A, SCN9A, SEMA3C, SEMA3D, SIRT3, STK11, STK11, SYNGAP1, TOPORS, and VCAN proteins.

[0004] In certain embodiments, a method of treating a disease or condition in a subject in need thereof by modulating expression of a target protein in the cells of the subject, the method comprising contacting the cells of the subject with a therapeutic agent that modulates splicing of a nonsense-mediated mRNA decay-directed exon (NMD exon) from an mRNA in the cell that contains the NMD exon and encodes a target protein, thereby modulating the level of processed mRNA encoding the target protein and modulating expression of the target protein in the cells of the subject, the target protein being selected from the group consisting of AKT3, CACNA1, and AKT3. A, CBS, CD46, CFH, CHD2, CLN3, COL11A2, COL4A3, COL4A4, COL4A4, CR1, CRX, CYP2J2, DHDDS, DNAJC8, EIF2AK3, ERN1, GALE, GUCY2F, GUCY2F, HEXA, HEXA, MAPK3, MBD5, MBD5, MBD5, MUT, MYH14, MYO6, NF1, NF2, NIPBL, NR1H4, NSD1, NSD1, NSD1, NSD1, OPA1, OPA1, PCCA, PKP2, PPARA, PRPF3, PRPF3, SCN2A, SCN8A, SCN8A, SCN9A, SEMA3C, SEMA3D, SIRT3 , STK11, STK11, SYNGAP1, TOPORS, and VCAN proteins.

[0005]

[0005] In some embodiments, the therapeutic agent (a) binds to a targeting portion of the mRNA encoding the target protein, (b) modulates the binding of a factor involved in splicing of the NMD exon, or (c) a combination of (a) and (b).

[0006] In some embodiments, the therapeutic agent interferes with binding of a factor involved in splicing of the NMD exon to the region of the targeting moiety. In some embodiments, the targeting moiety is proximal to the NMD exon. In some embodiments, the targeting moiety is up to about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides, about 600 nucleotides, about 500 nucleotides, about 400 nucleotides, about 300 nucleotides, about 200 nucleotides, about 100 nucleotides, about 80 nucleotides, about 70 nucleotides, about 60 nucleotides, or about 50 nucleotides upstream of the 5' end of the NMD exon. In some embodiments, the targeting moiety is at least about 1500, 1000, 800, 700, 600, 500, 400, 300, 200, 100, 80, 70, 60, 50, 40, 30, 20, 10, 5, 4, 2, or 1 nucleotide upstream of the 5' end of the NMD exon. In some embodiments, the targeting moiety is at most about 1500, 1000, 800, 700, 600, 500, 400, 300, 200, 100, 80, 70, 60, or 50 nucleotides downstream of the 3' end of the NMD exon.In some embodiments, the targeting moiety is at least about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides, about 600 nucleotides, about 500 nucleotides, about 400 nucleotides, about 300 nucleotides, about 200 nucleotides, about 100 nucleotides, about 80 nucleotides, about 70 nucleotides, about 60 nucleotides, about 50 nucleotides, about 40 nucleotides, about 30 nucleotides, about 20 nucleotides, about 10 nucleotides, about 5 nucleotides, about 4 nucleotides, about 2 nucleotides, or about 1 nucleotide downstream of the 3' end of the NMD exon.

[0007] In some embodiments, the targeting moiety is GRCh38 / hg38:chr1 243564388; GRCh38 / hg38:chr19 13236618; GRCh38 / hg38:chr21 43060012; GRCh38 / hg38:chr1 207775610;GRCh38 / hg38:chr1 196675450;GRCh38 / hg38:chr15 92998149;GRCh38 / hg38:chr16 28479765;GRCh38 / hg38:chr6 33183698;GRCh38 / hg38:chr2 227296487;GRCh38 / hg38:chr2 227144833;GRCh38 / hg38:chr2 227015360;GRCh38 / hg38:chr1 207637688;GRCh38 / hg38:chr19 47835403;GRCh38 / hg38:chr1 59904516;GRCh38 / hg38:chr1 26442335;GRCh38 / hg38:chr1 28230252;GRCh38 / hg38:chr2 88582824;GRCh38 / hg38:chr17 64102804;GRCh38 / hg38:chr1 23798484;GRCh38 / hg38:chrX 109383446;GRCh38 / hg38:chrX 109439175;GRCh38 / hg38:chr15 72362466;GRCh38 / hg38:chr15 72345776;GR Ch38 / hg38:chr16 30115645;GRCh38 / hg38:chr2 148460219;GRCh38 / hg38:chr2 148490695;GRCh38 / hg38:chr2 148505761;GRCh38 / hg38:chr6 49436597;GRCh38 / hg38:chr19 50230825;GRCh38 / hg38:chr6 75867431;GRCh38 / hg38:chr17 31249955;GRCh38 / hg38:chr22 29628658;GRCh38 / hg38:chr5 37048127;GRCh38 / hg38:chr12 100499841;GRCh38 / hg38:chr5 177169394;GRCh38 / hg38:chr5 177200761;GRCh38 / hg38:chr5 177247924;GRCh38 / hg38:chr5 177275947;GRCh38 / hg38:chr3 193628509;GRCh38 / hg38:chr3 193603500;GRCh38 / hg38:chr13 100305751;GRCh38 / hg38:chr12 32894778;GRCh38 / hg38:chr22 46203575;GRCh38 / hg38:chr1 150327557;GRCh38 / hg38:chr1 150330401;GRCh38 / hg38:chr2 165327155;GRCh38 / hg38:chr12 51688758;GRCh38 / hg38:chr12 51780202;GRCh38 / hg38:chr2 166304329;GRCh38 / hg38:chr7 80794957;GRCh38 / hg38:chr7 85059541;GRCh38 / hg38:chr11 226081;GRCh38 / hg38:chr19 1216268;GRCh38 / hg38:chr19 1221621;GRCh38 / hg38:chr6 33448789;GRCh38 / hg38:chr9 32551469;and GRCh38 / hg38:chr5 83544965, and are up to about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides, about 600 nucleotides, about 500 nucleotides, about 400 nucleotides, about 300 nucleotides, about 200 nucleotides, about 100 nucleotides, about 80 nucleotides, about 70 nucleotides, about 60 nucleotides, or about 50 nucleotides upstream of a genomic site selected from the group consisting of:

[0008] In some embodiments, the targeting moiety is GRCh38 / hg38:chr1 243564388; GRCh38 / hg38:chr19 13236618; GRCh38 / hg38:chr21 43060012; GRCh38 / hg38:chr1 207775610;GRCh38 / hg38:chr1 196675450;GRCh38 / hg38:chr15 92998149;GRCh38 / hg38:chr16 28479765;GRCh38 / hg38:chr6 33183698;GRCh38 / hg38:chr2 227296487;GRCh38 / hg38:chr2 227144833;GRCh38 / hg38:chr2 227015360;GRCh38 / hg38:chr1 207637688;GRCh38 / hg38:chr19 47835403;GRCh38 / hg38:chr1 59904516;GRCh38 / hg38:chr1 26442335;GRCh38 / hg38:chr1 28230252;GRCh38 / hg38:chr2 88582824;GRCh38 / hg38:chr17 64102804;GRCh38 / hg38:chr1 23798484;GRCh38 / hg38:chrX 109383446;GRCh38 / hg38:chrX 109439175;GRCh38 / hg38:chr15 72362466;GRCh38 / hg38:chr15 72345776;GRCh38 / hg38:chr16 30115645;GRCh38 / hg38:chr2 148460219;GRCh38 / hg38:chr2 148490695;GRCh38 / hg38:chr2 148505761;GRCh38 / hg38:chr6 49436597;GRCh38 / hg38:chr19 50230825;GRCh38 / hg38:chr6 75867431;GRCh38 / hg38:chr 17 31249955;GRCh38 / hg38:chr22 29628658;GRCh38 / hg38:chr5 37048127;GRCh38 / hg38:chr12 100499841;GRCh38 / hg38:chr5 177169394;GRCh38 / hg38:chr5 177200761;GRCh38 / hg38:chr5 177247924;GRCh38 / hg38:chr5 177275947;GRCh38 / hg38:chr3 193628509;GRCh38 / hg38:chr3 193603500;GRCh38 / hg38:chr13 100305751;GRCh38 / hg38:chr12 32894778;GRCh38 / hg38:chr22 46203575;GRCh38 / hg38:chr1 150327557;GRCh38 / hg38:chr1 150330401;GRCh38 / hg38:chr2 165327155;GRCh38 / hg38:chr12 51688758;GRCh38 / hg38:chr12 51780202;GRCh38 / hg38:chr2 166304329;GRCh38 / hg38:chr7 80794957;GRCh38 / hg38:chr7 85059541; GRCh38 / hg38:chr11 226081; GRCh38 / hg38:chr19 1216268; GRCh38 / hg38:chr19 1221621; GRCh38 / hg38:chr6 33448789; GRCh38 / hg38:chr9 32551469; and GRCh38 / hg38:chr5 83544965, about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides, about 600 nucleotides, about 500 nucleotides, about 400 nucleotides, about 300 nucleotides, about 200 nucleotides, about 100 nucleotides, about 80 nucleotides, about 70 nucleotides, about 60 nucleotides, or about 50 nucleotides upstream of a genomic site selected from the group consisting of GRCh38 / hg38:chr11 226081; GRCh38 / hg38:chr19 1216268; GRCh38 / hg38:chr19 1221621; GRCh38 / hg38:chr6 33448789; GRCh38 / hg38:chr9 32551469; and GRCh38 / hg38:chr5 83544965.

[0009] In some embodiments, the targeting moiety is GRCh38 / hg38:chr1 243564285; GRCh38 / hg38:chr19 13236449; GRCh38 / hg38:chr21 43059730; GRCh38 / hg38:chr1 207775745;GRCh38 / hg38:chr1 196675529;GRCh38 / hg38:chr15 92998261;GRCh38 / hg38:chr16 28479644;GRCh38 / hg38:chr6 33183634;GRCh38 / hg38:chr2 227296526;GRCh38 / hg38:chr2 227144653;GRCh38 / hg38:chr2 227015283;GRCh38 / hg38:chr1 207637848;GRCh38 / hg38:chr19 47835579;GRCh38 / hg38:chr1 59904366;GRCh38 / hg38:chr1 26442372;GRCh38 / hg38:chr1 28230131;GRCh38 / hg38:chr2 88582755;GRCh38 / hg38:chr17 64102673;GRCh38 / hg38:chr1 23798311;GRCh38 / hg38:chrX 109383365;GRCh38 / hg38:chrX 109439038;GRCh38 / hg38:chr15 72362376;GRCh38 / hg38:chr15 72345677;GRCh38 / hg38:chr16 30115595;GRCh38 / hg38:chr2 148460304;GRCh38 / hg38:chr2 148490787;GRCh38 / hg38:chr2 148505830;GRCh38 / hg38:chr6 49436522;GRCh38 / hg38:chr19 50230999;GRCh38 / hg38:chr6 75867523;GRCh38 / hg38:chr17 31250125;GRCh38 / hg38:chr22 29628773;GRCh38 / hg38:chr5 37048354;GRCh38 / hg38:chr12 100500024;GRCh38 / hg38:chr5 177169559;GRCh38 / hg38:chr5 177200783;GRCh38 / hg38:chr5 177248079;GRCh38 / hg38:chr5 177276101 ;GRCh38 / hg38:chr3 193628616;GRCh38 / hg38:chr3 193603557;GRCh38 / hg38:chr13 100305834;GRCh38 / hg38:chr12 32894516;GRCh38 / hg38:chr22 46203752;GRCh38 / hg38:chr1 150327652;GRCh38 / hg38:chr1 150330498;GRCh38 / hg38:chr2 165327202;GRCh38 / hg38:chr12 51688849;GRCh38 / hg38:chr12 51780271;GRCh38 / hg38:chr2 166304238;GRCh38 / hg38:chr7 80794854;GRCh38 / hg38:chr7 85059498;GRCh38 / hg38:chr11 225673;GRCh38 / hg38:chr19 1216398;GRCh38 / hg38:chr19 1221846;GRCh38 / hg38:chr6 33448868;GRCh38 / hg38:chr9 32551365; and GRCh38 / hg38:chr5 The sequence is located up to about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides, about 600 nucleotides, about 500 nucleotides, about 400 nucleotides, about 300 nucleotides, about 200 nucleotides, about 100 nucleotides, about 80 nucleotides, about 70 nucleotides, about 60 nucleotides, or about 50 nucleotides downstream of a genomic site selected from the group consisting of: 83545070.

[0010] In some embodiments, the targeting moiety is GRCh38 / hg38:chr1 243564285; GRCh38 / hg38:chr19 13236449; GRCh38 / hg38:chr21 43059730; GRCh38 / hg38:chr1 207775745;GRCh38 / hg38:chr1 196675529;GRCh38 / hg38:chr15 92998261;GRCh38 / hg38:chr16 28479644;GRCh38 / hg38:chr6 33183634;GRCh38 / hg38:chr2 227296526;GRCh38 / hg38:chr2 227144653;GRCh38 / hg38:chr2 227015283;GRCh38 / hg38:chr1 207637848;GRCh38 / hg38:chr19 47835579;GRCh38 / hg38:chr1 59904366;GRCh38 / hg38:chr1 26442372;GRCh38 / hg38:chr1 28230131;GRCh38 / hg38:chr2 88582755;GRCh38 / hg38:chr17 64102673;GRCh38 / hg38:chr1 23798311;GRCh38 / hg38:chrX 109383365;GRCh38 / hg38:chrX 109439038;GRCh38 / hg38:chr15 72362376;GRCh38 / hg38:chr15 72345677;GRCh38 / hg38:chr16 30115595;GRCh38 / hg38:chr2 148460304;GRCh38 / hg38:chr2 148490787;GRCh38 / hg38:chr2 148505830;GRCh38 / hg38:chr6 49436522;GRCh38 / hg38:chr19 50230999;GRCh38 / hg38:chr6 75867523;GRCh38 / hg38:chr17 31250125;GRCh38 / hg38:chr22 29628773;GRCh38 / hg38:chr5 37048354;GRCh38 / hg38:chr12 100500024;GRCh38 / hg38:chr5 177169559;GRCh38 / hg38:chr5 177200783;GRCh38 / hg38:chr5 177248079;GRCh38 / hg38:chr5 177276101;GRCh38 / hg38:chr3 193628616;GRCh38 / hg38:chr3 193603557;GRCh38 / hg38:chr13 100305834;GRCh38 / hg38:chr12 32894516;GRCh38 / hg38:chr22 46203752;GRCh38 / hg38:chr1 150327652;GRCh38 / hg38:chr1 150330498;GRCh38 / hg 38:chr2 165327202;GRCh38 / hg38:chr12 51688849;GRCh38 / hg38:chr12 51780271;GRCh38 / hg38:chr2 166304238;GRCh38 / hg38:chr7 80794854;GRCh38 / hg38:chr7 85059498;GRCh38 / hg38:chr11 225673;GRCh38 / hg38:chr19 1216398;GRCh38 / hg38:chr19 1221846;GRCh38 / hg38:chr6 33448868;GRCh38 / hg38:chr9 32551365; and GRCh38 / hg38:chr5 83545070;

[0011] In some embodiments, the targeting moiety is located in an intron region between two standard exon regions of an mRNA encoding a target protein, the intron region containing an NMD exon. In some embodiments, the targeting moiety at least partially overlaps with an NMD exon. In some embodiments, the targeting moiety at least partially overlaps with an intron upstream or downstream of an NMD exon. In some embodiments, the targeting moiety comprises a 5' NMD exon-intron junction or a 3' NMD exon-intron junction. In some embodiments, the targeting moiety is within an NMD exon. In some embodiments, the targeting moiety comprises about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 or more consecutive nucleotides of an NMD exon.

[0012] In some embodiments, the mRNA encoding the target protein comprises a sequence having at least about 80%, 85%, 90%, 95%, 97%, or 100% sequence identity to a sequence selected from the group consisting of SEQ ID NOs: 135 to 191. In some embodiments, the mRNA encoding the target protein is encoded by a gene sequence having at least about 80%, 85%, 90%, 95%, 97%, or 100% sequence identity to a sequence selected from the group consisting of SEQ ID NOs: 1-5, 12, 19-21, 25, 26, 28, 30, 33, 35, 38, 40, 41, 44, 45, 51, 53, 55-57, and 192-211. In some embodiments, the targeting portion of the mRNA comprises a sequence having at least 80%, 85%, 90%, 95%, 97%, or 100% sequence identity to a region comprising at least 8 contiguous nucleic acids of a sequence selected from the group consisting of SEQ ID NOs: 135-191. In some embodiments, the agent is an antisense oligomer (ASO), and the ASO comprises a sequence that is at least about 80%, 85%, 90%, 95%, 97%, or 100% complementary to at least 8 contiguous nucleic acids of a sequence selected from the group consisting of SEQ ID NOs: 135-191.

[0013] In some embodiments, the targeting portion of the mRNA is selected from the group consisting of GRCh38 / hg38:chr1 243564285 243564388; GRCh38 / hg38:chr19 13236449 13236618; GRCh38 / hg38:chr21 43059730 43060012; GRCh38 / hg38:chr1 207775610 207775745; GRCh38 / hg38:chr1 196675450 196675529; GRCh38 / hg38:chr15 92998149 92998261; GRCh38 / hg38:chr16 28479644 28479765;GRCh38 / hg38:chr6 33183634 33183698;GRCh38 / hg38:chr2 227296487 227296526;GRCh38 / hg38:chr2 227144653 227144833;GRCh38 / hg38:chr2 227015283 227015360;GRCh38 / hg38:chr1 207637688 207637848;GRCh38 / hg38:chr19 47835403 47835579;GRCh38 / hg38:chr1 59904366 59904516;GRCh38 / hg38:chr1 26442335 26442372;GRCh38 / hg38:chr1 28230131 28230252 ;GRCh38 / hg38:chr2 88582755 88582824;GRCh38 / hg38:chr17 64102673 64102804;GRCh38 / hg38:chr1 23798311 23798484;GRCh38 / hg38:chrX 109383365 109383446;GRCh38 / hg38:chrX 109439038 109439175;GRCh38 / hg38:chr15 72362376 72362466;GRCh38 / hg38:chr15 72345677 72345776;GRCh38 / hg38:chr16 30115595 30115645;GRCh38 / hg38:chr2 148460219 148460304;GRCh38 / hg38:chr2 148490695 148490787;GRCh38 / hg38:chr2 148505761 148505830;GRCh38 / hg38:chr6 49436522 49436597;GRCh38 / hg38:chr19 50230825 50230999;GRCh38 / hg38:chr6 75867431 75867523;GRCh38 / hg38:chr17 31249955 31250125;GRCh38 / hg38:chr22 29628658 29628773;GRCh38 / hg38:chr5 37048127 37048354;GRCh38 / hg38:chr12 100499841 100500024;GRCh38 / hg38:chr5 177169394 177169559;GRCh38 / hg38:chr5 177200761 177200783;GRCh38 / hg38:chr5 177247924 177248079;GRCh38 / hg38:chr5 177275947 177276101;GRCh38 / hg38:chr3 193628509 193628616;GRCh38 / hg38:chr3 193603500 193603557;GRCh38 / hg38:chr13 100305751 100305834;GRCh38 / hg38:chr12 32894516 32894778;GRCh38 / hg38:chr22 46203575 46203752;GRCh38 / hg38:chr1 150327557 150327652;GRCh38 / hg38:chr1 150330401 150330498;GRCh38 / hg38:chr2 165327155 165327202;GRCh38 / hg38:chr12 51688758 51688849;GRCh38 / hg38:chr12 51780202 51780271;GRCh38 / hg38:chr2 166304238 166304329;GRCh38 / hg38:chr7 80794854 80794957;GRCh38 / hg38:chr7 85059498 85059541;GRCh38 / hg38:chr11 225673 226081;GRCh38 / hg38:chr19 1216268 1216398;GRCh38 / hg38:chr19 1221621 1221846;GRCh38 / hg38:chr6 33448789 33448868;GRCh38 / hg38:chr9 32551365 32551469; and GRCh38 / hg38:chr5 83544965 83545070 within a nonsense-mediated RNA decay-inducible exon.

[0014] In some embodiments, the targeting portion of the mRNA is GRCh38 / hg38:chr1 243564285 243564388; GRCh38 / hg38:chr19 13236449 13236618; GRCh38 / hg38:chr21 43059730 43060012; GRCh38 / hg38:chr1 207775610 207775745; GRCh38 / hg38:chr1 19667545 0 196675529;GRCh38 / hg38:chr15 92998149 92998261;GRCh38 / hg38:chr16 28479644 28479765;GRCh38 / hg38:chr6 33183634 33183698;GRCh38 / hg38:chr2 227296487 227296526;GRCh38 / hg38:chr2 227144653 227144833;GRCh38 / hg38:chr2 227015283 227015360;GRCh38 / hg38:chr1 207637688 207637848;GRCh38 / hg38:chr19 47835403 47835579;GRCh38 / hg38:chr1 59904366 59904516;GRCh38 / hg38:chr1 26442335 26442372;GRCh38 / hg38:chr1 28230131 28230252 ;GRCh38 / hg38:chr2 88582755 88582824;GRCh38 / hg38:chr17 64102673 64102804;GRCh38 / hg38:chr1 23798311 23798484;GRCh38 / hg38:chrX 109383365 109383446;GRCh38 / hg38:chrX 109439038 109439175;GRCh38 / hg38:chr15 72362376 72362466;GRCh38 / hg38:chr15 72345677 72345776;GRCh38 / hg38:chr16 30115595 30115645;GRCh38 / hg38:chr2 148460219 148460304;GRCh38 / hg38:chr2 148490695 148490787;GRCh38 / hg38:chr2 148505761 148505830;GRCh38 / hg38:chr6 49436522 49436597;GRCh38 / hg38:chr19 50230825 50230999;GRCh38 / hg38:chr6 75867431 75867523;GRCh38 / hg38:chr17 31249955 31250125;GRCh38 / hg38:chr22 29628658 29628773;GRCh38 / hg38:chr5 37048127 37048354;GRCh38 / hg38:chr12 100499841 100500024;GRCh38 / hg38:chr5 177169394 177169559;GRCh38 / hg38:chr5 177200761 177200783;GRCh38 / hg38:chr5 177247924 177248079;GRCh38 / hg38:chr5 177275947 177276101;GRCh38 / hg38:chr3 193628509 193628616;GRCh38 / hg38:chr3 193603500 193603557;GRCh38 / hg38:chr13 100305751 100305834;GRCh38 / hg38:chr12 32894516 32894778;GRCh38 / hg38:chr22 46203575 46203752;GRCh38 / hg38:chr1 150327557 150327652;GRCh38 / hg38:chr1 150330401 150330498;GRCh38 / hg38:chr2 165327155 165327202;GRCh38 / hg38:chr12 51688758 51688849;GRCh38 / hg38:chr12 51780202 51780271;GRCh38 / hg38:chr2 166304238 166304329;GRCh38 / hg38:chr7 80794854 80794957;GRCh38 / hg38:chr7 85059498 85059541;GRCh38 / hg38:chr11 225673 226081;GRCh38 / hg38:chr19 1216268 1216398;GRCh38 / hg38:chr19 1221621 1221846;GRCh38 / hg38:chr6 33448789 33448868;GRCh38 / hg38:chr9 32551365 32551469; and GRCh38 / hg38:chr5 83544965 83545070, upstream or downstream of a nonsense-mediated RNA decay-inducible exon selected from the group consisting of

[0015] In some embodiments, the targeting portion of the mRNA is GRCh38 / hg38:chr1 243564285 243564388; GRCh38 / hg38:chr19 13236449 13236618; GRCh38 / hg38:chr21 43059730 43060012; GRCh38 / hg38:chr1 207775610 207775745; GRCh38 / hg38:chr1 196675450 196675529;GRCh38 / hg38:chr15 92998149 92998261;GRCh38 / hg38:chr16 28479644 28479765;GRCh38 / hg38:chr6 33183634 33183698;GRCh38 / hg38:chr2 227296487 227296526;GRCh38 / hg38:chr2 227144653 227144833;GRCh38 / hg38:chr2 227015283 227015360;GRCh38 / hg38:chr1 207637688 207637848;GRCh38 / hg38:chr19 47835403 47835579;GRCh38 / hg38:chr1 59904366 59904516;GRCh38 / hg38:chr1 26442335 26442372;GRCh38 / hg38:chr1 28230131 28230252 ;GRCh38 / hg38:chr2 88582755 88582824;GRCh38 / hg38:chr17 64102673 64102804;GRCh38 / hg38:chr1 23798311 23798484;GRCh38 / hg38:chrX 109383365 109383446;GRCh38 / hg38:chrX 109439038 109439175;GRCh38 / hg38:chr15 72362376 72362466;GRCh38 / hg38:chr15 72345677 72345776;GRCh38 / hg38:chr16 30115595 30115645;GRCh38 / hg38:chr2 148460219 148460304;GRCh38 / hg38:chr2 148490695 148490787;GRCh38 / hg38:chr2 148505761 148505830;GRCh38 / hg38:chr6 49436522 49436597;GRCh38 / hg38:chr19 50230825 50230999;GRCh38 / hg38:chr6 75867431 75867523;GRCh38 / hg38:chr17 31249955 31250125;GRCh38 / hg38:chr22 29628658 29628773;GRCh38 / hg38:chr5 37048127 37048354;GRCh38 / hg38:chr12 100499841 100500024;GRCh38 / hg38:chr5 177169394 177169559;GRCh38 / hg38:chr5 177200761 177200783;GRCh38 / hg38:chr5 177247924 177248079;GRCh38 / hg38:chr5 177275947 177276101;GRCh38 / hg38:chr3 193628509 193628616;GRCh38 / hg38:chr3 193603500 193603557;GRCh38 / hg38:chr13 100305751 100305834;GRCh38 / hg38:chr12 32894516 32894778;GRCh38 / hg38:chr22 46203575 46203752;GRCh38 / hg38:chr1 150327557 150327652;GRCh38 / hg38:chr1 150330401 150330498;GRCh38 / hg38:chr2; 165327155 165327202;GRCh38 / hg38:chr12 51688758 51688849;GRCh38 / hg38:chr12 51780202 51780271;GRCh38 / hg38:chr2 166304238 166304329;GRCh38 / hg38:chr7 80794854 80794957;GRCh38 / hg38:chr7 85059498 85059541;GRCh38 / hg38:chr11 225673 226081;GRCh38 / hg38:chr19 1216268 1216398;GRCh38 / hg38:chr19 1221621 1221846;GRCh38 / hg38:chr6 334 48789 33448868;GRCh38 / hg38:chr9 32551365 32551469; and GRCh38 / hg38:chr5 83544965 83545070.

[0016]

[0016] In some embodiments, the target protein produced is a full-length or wild-type protein.

[0017] In some embodiments, a therapeutic agent promotes the elimination of an NMD exon from processed mRNA encoding a target protein. In some embodiments, the elimination of an NMD exon from processed mRNA encoding a target protein in cells contacted with a therapeutic agent is about 1.1 to about 10-fold, about 1.5 to about 10-fold, about 2 to about 10-fold, about 3 to about 10-fold, about 4 to about 10-fold, about 1.1 to about 5-fold, about 1.1 to about 6-fold, about 1.1 to about 7-fold, about 1.1 to about 8-fold, about 1.1 to about 9-fold, about 1.1 to about 10-fold, about 1.1 to about 20-fold, about 1.1 to about 25-fold, about 1.1 to about 30-fold, about 1.1 to about 35-fold, about 1.1 to about 40-fold, about 1.1 to about 50-fold, about 1.1 to about 60-fold, about 1.1 to about 70-fold, about 1.1 to about 100-fold, about 1.1 to about 25-fold, about 1.1 to about 35-fold, about 1.1 to about 40-fold, about 1.1 to about 50-fold, about 1.1 to about 60-fold, about 1.1 to about 70-fold, about 1.1 to about 10 ... about 8-fold, about 1.1 to about 9-fold, about 2 to about 5-fold, about 2 to about 6-fold, about 2 to about 7-fold, about 2 to about 8-fold, about 2 to about 9-fold, about 3 to about 6-fold, about 3 to about 7-fold, about 3 to about 8-fold, about 3 to about 9-fold, about 4 to about 7-fold, about 4 to about 8-fold, about 4 to about 9-fold, at least about 1.1-fold, at least about 1.5-fold, at least about 2-fold, at least about 2.5-fold, at least about 3-fold, at least about 3.5-fold, at least about 4-fold, at least about 5-fold, or at least about 10-fold increase. In some embodiments, the therapeutic agent increases the level of processed mRNA encoding the target protein in the cell. In some embodiments, the level of processed mRNA encoding the target protein produced in cells contacted with a Therapeutic Agent is about 1.1 to about 10-fold, about 1.5 to about 10-fold, about 2 to about 10-fold, about 3 to about 10-fold, about 4 to about 10-fold, about 1.1 to about 5-fold, about 1.1 to about 6-fold, about 1.1 to about 7-fold, about 1.1 to about 8-fold, about 1.1 to about 9-fold, about 1.1 to about 10-fold, about 1.1 to about 11-fold, about 1.1 to about 12-fold, about 1.1 to about 13-fold, about 1.1 to about 14-fold, about 1.1 to about 15-fold, about 1.1 to about 16-fold, about 1.1 to about 17-fold, about 1.1 to about 18-fold, about 1.1 to about 19-fold, about 1.1 to about 20-fold, about 1.1 to about 21-fold, about 1.1 to about 22-fold, about 1.1 to about 23-fold, about 1.1 to about 24-fold, about 1.1 to about 25-fold, about 1.1 to about 26-fold, about 1.1 to about 27-fold, about 1.1 to about 28-fold, about 1.1 to about 29-fold, about 1.1 to about 30-fold, about 1.1 to about 31-fold, about 1.1 to about 32-fold, about 1.1 to about 33-fold, about 1.1 to about 34-fold, about 1.1 to about 35-fold, about 1.1 to about 36-fold, about 1.1 to about 37-fold, about an increase of 1 to about 9 fold, about 2 to about 5 fold, about 2 to about 6 fold, about 2 to about 7 fold, about 2 to about 8 fold, about 2 to about 9 fold, about 3 to about 6 fold, about 3 to about 7 fold, about 3 to about 8 fold, about 3 to about 9 fold, about 4 to about 7 fold, about 4 to about 8 fold, about 4 to about 9 fold, at least about 1.1 fold, at least about 1.5 fold, at least about 2 fold, at least about 2.5 fold, at least about 3 fold, at least about 3.5 fold, at least about 4 fold, at least about 5 fold, or at least about 10 fold. In some embodiments, the therapeutic agent increases expression of the target protein in the cell.In some embodiments, the level of target protein produced in cells contacted with a Therapeutic Agent is about 1.1 to about 10 fold, about 1.5 to about 10 fold, about 2 to about 10 fold, about 3 to about 10 fold, about 4 to about 10 fold, about 1.1 to about 5 fold, about 1.1 to about 6 fold, about 1.1 to about 7 fold, about 1.1 to about 8 fold, about 1.1 to about 9 fold, about 2 to about 5 fold, about 2 to about 6 fold, about 2 to about 7 fold, about 2 to about 8 fold, about 2 to about 9 ... to about 6-fold, about 2 to about 7-fold, about 2 to about 8-fold, about 2 to about 9-fold, about 3 to about 6-fold, about 3 to about 7-fold, about 3 to about 8-fold, about 3 to about 9-fold, about 4 to about 7-fold, about 4 to about 8-fold, about 4 to about 9-fold, at least about 1.1-fold, at least about 1.5-fold, at least about 2-fold, at least about 2.5-fold, at least about 3-fold, at least about 3.5-fold, at least about 4-fold, at least about 5-fold, or at least about 10-fold increase.

[0017]

[0018] In some embodiments, the disease or condition is caused by a loss-of-function mutation in the target protein.

[0019] In some embodiments, the disease or condition is associated with haploinsufficiency of a gene encoding a target protein, and the subject has a first allele that encodes a functional target protein and a second allele that results in the target protein being absent or produced at reduced levels, or a second allele that encodes a non-functional or partially functional target protein. In some embodiments, the disease or condition is associated with Sotos syndrome 1; Beckwith-Wiedemann syndrome; familial hemiplegic migraine 1; paroxysmal ataxia type 2; pediatric ataxia syndrome. early-onset epileptic encephalopathy; Wagner syndrome 1; optic atrophy type 1; Alport syndrome; arrhythmogenic right ventricular dysplasia 9; neurofibromatosis type 1; early infantile epileptic encephalopathy 11; benign familial infantile seizures 3; cognitive impairment with or without cerebellar ataxia; early infantile epileptic encephalopathy 13; benign familial infantile seizures 5; pathway (CNS); 16p11.2 deletion syndrome; autosomal dominant mental retardation 1; retinitis pigmentosa 18; retinitis pigmentosa 31; autosomal dominant hearing loss 13; cone-rod retinal dystrophy 2; autosomal dominant hearing loss 4A; peripheral neuropathy, myopathy, hoarseness, and hearing loss; autosomal dominant hearing loss 22; neurofibromatosis type 2; autosomal dominant mental retardation 5; generalized epilepsy with febrile seizures plus type 7; and familial febrile seizures 3B.

[0018]

[0020] In some embodiments, the disease or condition is associated with an autosomal recessive mutation in a gene encoding a target protein, and the subject has (i) a first allele in which the target protein is not produced or is produced at a reduced level compared to the wild-type allele, or (ii) the produced target protein is non-functional or partially functional compared to the wild-type allele, and (iii) a second allele in which the target protein is produced at a reduced level compared to the wild-type allele and the produced target protein is at least partially functional compared to the wild-type allele, or (iv) the produced target protein is partially functional compared to the wild-type allele. In some embodiments, the disease or condition is selected from the group consisting of Alport syndrome; neuronal ceroid lipofuscinosis 3; galactose epimerase deficiency; B6-responsive and non-responsive homocystinuria; methylmalonic aciduria; propionic acidemia; retinitis pigmentosa 59; Tay-Sachs disease; congenital insensitivity to pain; and autosomal recessive HSAN2D.

[0019]

[0021] In some embodiments, a therapeutic agent promotes the exclusion of an NMD exon from processed mRNA encoding a target protein, increasing expression of the target protein in cells. In some embodiments, a therapeutic agent inhibits the exclusion of an NMD exon from processed mRNA encoding a target protein. In some embodiments, the exclusion of an NMD exon from processed mRNA encoding a target protein in cells contacted with a therapeutic agent is about 1.1 to about 10-fold, about 1.5 to about 10-fold, about 2 to about 10-fold, about 3 to about 10-fold, about 4 to about 10-fold, about 1.1 to about 5-fold, about 1.1 to about 6-fold, about 1.1 to about 7-fold, about 1.1 to about 8 fold, about 1.1 to about 9 fold, about 2 to about 5 fold, about 2 to about 6 fold, about 2 to about 7 fold, about 2 to about 8 fold, about 2 to about 9 fold, about 3 to about 6 fold, about 3 to about 7 fold, about 3 to about 8 fold, about 3 to about 9 fold, about 4 to about 7 fold, about 4 to about 8 fold, about 4 to about 9 fold, about 1.1 fold or less, about 1.5 fold or less, about 2 fold or less, about 2.5 fold or less, about 3 fold or less, about 3.5 fold or less, about 4 fold or less, about 5 fold or less, or about 10 fold or less. In some embodiments, the therapeutic agent reduces the level of processed mRNA encoding the target protein in the cell.In some embodiments, the level of processed mRNA encoding the target protein in cells contacted with a Therapeutic Agent is about 1.1 to about 10 fold, about 1.5 to about 10 fold, about 2 to about 10 fold, about 3 to about 10 fold, about 4 to about 10 fold, about 1.1 to about 5 fold, about 1.1 to about 6 fold, about 1.1 to about 7 fold, about 1.1 to about 8 fold, about 1.1 to about 1 / 9, about 2 to about 1 / 5, about 2 to about 1 / 6, about 2 to about 1 / 7, about 2 to about 1 / 8, about 2 to about 1 / 9, about 3 to about 1 / 6, about 3 to about 1 / 7, about 3 to about 1 / 8, about 3 to about 1 / 9, about 4 to about 1 / 7, about 4 to about 1 / 8, about 4 to about 1 / 9, about 1.1 or less, about 1.5 or less, about 2 or less, about 2.5 or less, about 1 / 3 or less, about 3.5 or less, about 1 / 4 or less, about 1 / 5 or less, or about 10. It is less than one-third.

[0020]

[0022] In some embodiments, a therapeutic agent reduces expression of a target protein in a cell. In some embodiments, the level of target protein produced in a cell contacted with a therapeutic agent is about 1.1 to about 10 fold, about 1.5 to about 10 fold, about 2 to about 10 fold, about 3 to about 10 fold, about 4 to about 10 fold, about 1.1 to about 5 fold, about 1.1 to about 6 fold, about 1.1 to about 7 fold, about 1.1 to about 8 fold, about 1.1 to about 9 fold, about 2 to about 5 fold, of about 1 / 2, about 2 to about 1 / 6, about 2 to about 1 / 7, about 2 to about 1 / 8, about 2 to about 1 / 9, about 3 to about 1 / 6, about 3 to about 1 / 7, about 3 to about 1 / 8, about 3 to about 1 / 9, about 4 to about 1 / 7, about 4 to about 1 / 8, about 4 to about 1 / 9, about 1.1 or less, about 1.5 or less, about 2 or less, about 2.5 or less, about 1 / 3 or less, about 3.5 or less, about 1 / 4 or less, about 1 / 5 or less, or about 1 / 10 or less.

[0021]

[0023] In some embodiments, the disease or condition is caused by a gain-of-function mutation in the target protein, hi some embodiments, the subject has an allele that causes the target protein to be produced at increased levels or encodes a mutant target protein that exhibits increased activity in the cell.

[0022]

[0024] In some embodiments, the therapeutic agent inhibits the removal of NMD exons from the processed mRNA encoding the target protein, thereby reducing the expression of the target protein in cells.In some embodiments, the target protein comprises SCN8A.In some embodiments, the disease or condition comprises a central nervous system disease.In some embodiments, the disease or condition comprises epilepsy.In some embodiments, the disease or condition comprises Dravet syndrome.

[0023]

[0025] In some embodiments, the therapeutic agent is an antisense oligomer (ASO) and the antisense oligomer comprises a backbone modification comprising a phosphorothioate linkage or a phosphorodiamidate linkage. In some embodiments, the therapeutic agent is an antisense oligomer (ASO) and the antisense oligomer comprises a phosphorodiamidate morpholino, locked nucleic acid, peptide nucleic acid, 2'-O-methyl, 2'-fluoro, or 2'-O-methoxyethyl moiety.

[0024]

[0026] In some embodiments, the therapeutic agent is an antisense oligomer (ASO), and the antisense oligomer comprises at least one modified sugar moiety. In some embodiments, each sugar moiety is a modified sugar moiety.

[0025]

[0027] In some embodiments, the therapeutic agent is an antisense oligomer (ASO), and the antisense oligomer is selected from the group consisting of 8 to 50 nucleobases, 8 to 40 nucleobases, 8 to 35 nucleobases, 8 to 30 nucleobases, 8 to 25 nucleobases, 8 to 20 nucleobases, 8 to 15 nucleobases, 9 to 50 nucleobases, 9 to 40 nucleobases, 9 to 35 nucleobases, 9 to 30 nucleobases, 9 to 25 nucleobases, 9 to 20 nucleobases, 9 to 15 nucleobases, 10 to 50 nucleobases, 10 to 40 ... The nucleic acid sequence may comprise from 1 to 35 nucleobases, 10 to 30 nucleobases, 10 to 25 nucleobases, 10 to 20 nucleobases, 10 to 15 nucleobases, 11 to 50 nucleobases, 11 to 40 nucleobases, 11 to 35 nucleobases, 11 to 30 nucleobases, 11 to 25 nucleobases, 11 to 20 nucleobases, 11 to 15 nucleobases, 12 to 50 nucleobases, 12 to 40 nucleobases, 12 to 35 nucleobases, 12 to 30 nucleobases, 12 to 25 nucleobases, 12 to 20 nucleobases, or 12 to 15 nucleobases.

[0026]

[0028] In some embodiments, the therapeutic agent is an antisense oligomer (ASO), and the antisense oligomer is at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% complementary to the targeted portion of the mRNA.

[0027]

[0029] In some embodiments, the method further comprises assessing the mRNA level or expression level of the target protein.

[0030] In some embodiments, the subject is a human. In some embodiments, the subject is a non-human animal. In some embodiments, the subject is a fetus, embryo, or child. In some embodiments, the cells are ex vivo. In some embodiments, the therapeutic agent is administered to the subject by intrathecal injection, intracerebroventricular injection, intraperitoneal injection, intramuscular injection, subcutaneous injection, intravitreal injection, or intravenous injection. In some embodiments, the method further comprises administering a second therapeutic agent to the subject.

[0028]

[0031] In some embodiments, the second therapeutic agent is a small molecule. In some embodiments, the second therapeutic agent is an antisense oligomer. In some embodiments, the second therapeutic agent corrects intron retention.

[0029]

[0032] In some embodiments, the disease or condition is 16p11.2 deletion syndrome; Alport syndrome; arrhythmogenic right ventricular dysplasia 9; neuronal ceroid lipofuscinosis 3; cognitive impairment with or without cerebellar ataxia; early infantile epileptic encephalopathy 13; benign familial infantile seizures 5; cone-rod retinal dystrophy 2; Cornelia de Lange; autosomal dominant hearing loss 13; autosomal dominant hearing loss 4A; peripheral neuropathy, myopathy, hoarseness, and hearing loss; generalized epilepsy with febrile seizures plus type 7; familial febrile seizures 3B; congenital insensitivity to pain; autosomal recessive HSAN2D; pediatric The present invention is selected from the group consisting of: early-onset epileptic encephalopathy; early infantile epileptic encephalopathy 11; benign familial infantile seizures 3; galactose epimerase deficiency; B6-responsive and non-responsive homocystinuria; autosomal dominant mental retardation 1; autosomal dominant mental retardation 5; methylmalonic aciduria; familial hemiplegic migraine 1; paroxysmal ataxia type 2; NASH; neurofibromatosis type 1; neurofibromatosis type 2; optic atrophy type 1; propionic acidemia; retinitis pigmentosa 18; Sotos syndrome 1; Beckwith-Wiedemann syndrome; Tay-Sachs disease; and Wagner syndrome 1. Incorporation by Reference

[0033] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.

[0030]

[0034] The novel features of the present disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosure will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the disclosure are utilized, and the accompanying drawings. [Brief explanation of the drawings]

[0031] [Figure 1A]

[0035] Figure 1A shows a schematic diagram of target mRNAs containing nonsense-mediated RNA decay-inducible exons (NMD exon mRNAs) and therapeutic-agent-mediated elimination of nonsense-mediated mRNA decay-inducible exons, which increases expression of full-length target proteins or functional RNAs. Figure 1A shows a cell divided into nuclear and cytoplasmic compartments. In the nucleus, pre-mRNA transcripts of target genes undergo splicing to generate mRNA, which is transported to the cytoplasm and translated into target proteins. For this target gene, a portion of the mRNA contains nonsense-mediated mRNA decay-inducible exons that are degraded in the cytoplasm (NMD exon mRNAs), thus not resulting in target protein production. [Figure 1B]

[0036] Figure 1B shows an example of the same cell separated into nuclear and cytoplasmic compartments. Treatment with a therapeutic agent, such as an antisense oligomer (ASO), promotes nonsense-mediated mRNA decay-induced exon elimination, resulting in increased mRNA, which is translated into higher levels of target protein. [Figure 2]

[0037] Figure 2 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the CD46 gene. Identification of an NMD-induced exon in the CD46 gene using RNA sequencing is shown visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the CD46 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr1 207770363 207783291 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, targeting the transcript for NMD. [Figure 3]

[0038] Figure 3 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the COL11A2 gene. Identification of an NMD-induced exon in the COL11A2 gene using RNA sequencing is visualized in the UCSC Genome Browser. The top panel shows a scaled graphical representation of the COL11A2 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr6 33181172 33184144 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 4]

[0039] Figure 4 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the CR1 gene. Identification of an NMD-induced exon in the CR1 gene using RNA sequencing is visualized in the UCSC Genome Browser. The top panel shows a scaled graphical representation of the CR1 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr1 207630622 207639396 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 5]

[0040] Figure 5 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the CRX gene. Identification of an NMD-induced exon in the CRX gene using RNA sequencing is visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the CRX gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr19 47834545 47836242 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, targeting the transcript for NMD. [Figure 6]

[0041] Figure 6 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the DNAJC8 gene. Identification of an NMD-induced exon in the DNAJC8 gene using RNA sequencing is visualized in the UCSC Genome Browser. The top panel shows a scaled graphical representation of the DNAJC8 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr1 28229025 28232920 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, targeting the transcript for NMD. [Figure 7]

[0042] Figure 7 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the MYH14 gene. Identification of an NMD-induced exon in the MYH14 gene using RNA sequencing is visualized in the UCSC Genome Browser. The top panel shows a scaled graphical representation of the MYH14 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr19 50230625 50231929 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, targeting the transcript for NMD. [Figure 8]

[0043] Figure 8 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the SEMA3C gene. The identification of an NMD-induced exon in the SEMA3C gene using RNA sequencing is visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the SEMA3C gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr7 80789529 80798091 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (lower panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 9]

[0044] Figure 9 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the VCAN gene. Identification of an NMD-induced exon in the VCAN gene using RNA sequencing is visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the VCAN gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr5 83542270 83545536 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, targeting the transcript for NMD. [Figure 10]

[0045] Figure 10 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the OPAI gene. Identification of an NMD-induced exon in the OPAI gene using RNA sequencing is visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the OPAI gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr3 193626204 193631611, shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, targeting the transcript for NMD. [Figure 11]

[0046] Figure 11 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the COL4A3 gene. Identification of an NMD-induced exon in the COL4A3 gene using RNA sequencing is visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the COL4A3 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr2 227295318 227297673 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 12]

[0047] Figure 12 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the DHDDS gene. Identification of an NMD-induced exon in the DHDDS gene using RNA sequencing is visualized and shown in the UCSC genome browser. The top panel shows a scaled graphical representation of the DHDDS gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr1 26438286 26442730 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 13]

[0048] Figure 13 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the CFH gene. Identification of an NMD-induced exon in the CFH gene using RNA sequencing is visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the CFH gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr1 196673964 196675988 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 14]

[0049] Figure 14 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the AKT3 gene. The identification of an NMD-induced exon in the AKT3 gene using RNA sequencing is visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the AKT3 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr1 243563849 243572925 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 15]

[0050] Figure 15 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the TOPORS gene. The identification of an NMD-induced exon in the TOPORS gene using RNA sequencing is visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the TOPORS gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr9 32550970 32552433 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 16]

[0051] Figure 16 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the PRPF3 gene. Identification of an NMD-induced exon in the PRPF3 gene using RNA sequencing is visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the PRPF3 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr1 150325883 150328319 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, targeting the transcript for NMD. [Figure 17]

[0052] Figure 17 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the PRPF3 gene. Identification of an NMD-induced exon in the PRPF3 gene using RNA sequencing is visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the PRPF3 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr1 150328468 150332683 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 18]

[0053] Figure 18 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the NIPBL gene. Identification of an NMD-induced exon in the NIPBL gene using RNA sequencing is shown visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the NIPBL gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr5 37046201 37048501 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, targeting the transcript for NMD. [Figure 19]

[0054] Figure 19 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the CBS gene. Identification of an NMD-induced exon in the CBS gene using RNA sequencing is visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the CBS gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr21 43059305 43060440 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 20]

[0055] Figure 20 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the PKP2 gene. The identification of an NMD-induced exon in the PKP2 gene using RNA sequencing is visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the PKP2 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr12 32879034 32896508 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 21]

[0056] Figure 21 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the COL4A4 gene. Identification of an NMD-induced exon in the COL4A4 gene using RNA sequencing is visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the COL4A4 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr2 227144560 227147412, shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 22]

[0057] Figure 22 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the COL4A4 gene. Identification of an NMD-induced exon in the COL4A4 gene using RNA sequencing is visualized and shown in the UCSC genome browser. The top panel shows a scaled graphical representation of the COL4A4 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr2 227012299 227022047 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 23]

[0058] Figure 23 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the CYP2J2 gene. The identification of an NMD-induced exon in the CYP2J2 gene using RNA sequencing is visualized and shown in the UCSC genome browser. The top panel shows a scaled graphical representation of the CYP2J2 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr1 59901104 59904870 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 24]

[0059] Figure 24 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the PPARA gene. Identification of an NMD-induced exon in the PPARA gene using RNA sequencing is visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the PPARA gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr22 46198592 46215172 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 25]

[0060] Figure 25 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the SEMA3D gene. The identification of an NMD-induced exon in the SEMA3D gene using RNA sequencing is visualized and shown in the UCSC genome browser. The top panel shows a scaled graphical representation of the SEMA3D gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr7 85055860 85065423 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 26]

[0061] Figure 26 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the ERN1 gene. The identification of an NMD-induced exon in the ERN1 gene using RNA sequencing is visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the ERN1 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr17 64098242 64129975 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 27]

[0062] Figure 27 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the GUCY2F gene. The identification of an NMD-induced exon in the GUCY2F gene using RNA sequencing is visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the GUCY2F gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chrX 109382213 109385183 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 28]

[0063] Figure 28 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the GUCY2F gene. The identification of an NMD-induced exon in the GUCY2F gene using RNA sequencing is visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the GUCY2F gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chrx 109430397 109441350 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 29]

[0064] Figure 29 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the SCN2A gene. Identification of an NMD-induced exon in the SCN2A gene using RNA sequencing is visualized and shown in the UCSC Genome Browser. The top panel shows a scaled graphical representation of the SCN2A gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr2 165326986 165331329 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 30]

[0065] Figure 30 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the SCN8A gene. The identification of an NMD-induced exon in the SCN8A gene using RNA sequencing is visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the SCN8A gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr12 51687221 51689004 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 31]

[0066] Figure 31 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the SCN8A gene. Identification of an NMD-induced exon in the SCN8A gene using RNA sequencing is visualized and shown in the UCSC Genome Browser. The top panel shows a scaled graphical representation of the SCN8A gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr12 51774364 51786541 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 32]

[0067] Figure 32 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the SCN9A gene. Identification of an NMD-induced exon in the SCN9A gene using RNA sequencing is visualized and shown in the UCSC Genome Browser. The top panel shows a scaled graphical representation of the SCN9A gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr2 166304123 166305791 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 33]

[0068] Figure 33 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the CLN3 gene. The identification of an NMD-induced exon in the CLN3 gene using RNA sequencing is visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the CLN3 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr16 28477879 28482104 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 34]

[0069] Figure 34 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the MAPK3 gene. The identification of an NMD-induced exon in the MAPK3 gene using RNA sequencing is visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the MAPK3 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr16 30114710 30116635 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 35]

[0070] Figure 35 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the NF1 gene. Identification of an NMD-induced exon in the NF1 gene using RNA sequencing is shown visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the NF1 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr17 31249120 31252937 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 36]

[0071] Figure 36 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the MBD5 gene. Identification of an NMD-induced exon in the MBD5 gene using RNA sequencing is visualized and shown in the UCSC genome browser. The top panel shows a scaled graphical representation of the MBD5 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr2 148502511 148510059 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 37]

[0072] Figure 37 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the MBD5 gene. Identification of an NMD-induced exon in the MBD5 gene using RNA sequencing is visualized and shown in the UCSC genome browser. The top panel shows a scaled graphical representation of the MBD5 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr2 148458873 148462581 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 38]

[0073] Figure 38 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the MBD5 gene. Identification of an NMD-induced exon in the MBD5 gene using RNA sequencing is visualized and shown in the UCSC genome browser. The top panel shows a scaled graphical representation of the MBD5 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr2 148490596 148502435 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 39]

[0074] Figure 39 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the NF2 gene. The identification of an NMD-induced exon in the NF2 gene using RNA sequencing is visualized and shown in the UCSC genome browser. The top panel shows a scaled graphical representation of the NF2 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr22 29604114 29636750 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 40]

[0075] Figure 40 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the MYO6 gene. The identification of an NMD-induced exon in the MYO6 gene using RNA sequencing is visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the MYO6 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr6 75867107 75870646 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 41]

[0076] Figure 41 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the SYNGAP1 gene. Identification of an NMD-induced exon in the SYNGAP1 gene using RNA sequencing is shown visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the SYNGAP1 gene. Peaks corresponding to RNA sequencing reads were identified in intron GRCh38 / hg38:chr6 33447935 33451759, shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 42]

[0077] Figure 42 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the SIRT3 gene. The identification of an NMD-induced exon in the SIRT3 gene using RNA sequencing is visualized and shown in the UCSC genome browser. The top panel shows a scaled graphical representation of the SIRT3 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr11 224241 230451 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 43]

[0078] Figure 43 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the CACNA1A gene. The identification of an NMD-induced exon in the CACNA1A gene using RNA sequencing is visualized and shown in the UCSC genome browser. The top panel shows a scaled graphical representation of the CACNA1A gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr19 13235732 13241520 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 44]

[0079] Figure 44 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the CHD2 gene. Identification of an NMD-induced exon in the CHD2 gene using RNA sequencing is visualized and shown in the UCSC genome browser. The top panel shows a scaled graphical representation of the CHD2 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr15 92997404 92998498 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 45]

[0080] Figure 45 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the NSD1 gene. Identification of an NMD-induced exon in the NSD1 gene using RNA sequencing is visualized and shown in the UCSC genome browser. The top panel shows a scaled graphical representation of the NSD1 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr5 177136032 177191883 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 46]

[0081] Figure 46 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the NSD1 gene. Identification of an NMD-induced exon in the NSD1 gene using RNA sequencing is visualized and shown in the UCSC genome browser. The top panel shows a scaled graphical representation of the NSD1 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr5 177192021 177204119 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 47]

[0082] Figure 47 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the NSD1 gene. The identification of an NMD-induced exon in the NSD1 gene using RNA sequencing is visualized and shown in the UCSC genome browser. The top panel shows a scaled graphical representation of the NSD1 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr5 177246798 177248180 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 48]

[0083] Figure 48 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the NSD1 gene. The identification of an NMD-induced exon in the NSD1 gene using RNA sequencing is visualized and shown in the UCSC genome browser. The top panel shows a scaled graphical representation of the NSD1 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr5 177273786 177280564 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 49]

[0084] Figure 49 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the EIF2AK3 gene. The identification of an NMD-induced exon in the EIF2AK3 gene using RNA sequencing is visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the EIF2AK3 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr2 88579641 88583429 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 50]

[0085] Figure 50 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the GALE gene. The identification of an NMD-induced exon in the GALE gene using RNA sequencing is visualized and shown in the UCSC genome browser. The top panel shows a scaled graphical representation of the GALE gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr1 23798232 23798614 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 51]

[0086] Figure 51 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the HEXA gene. Identification of an NMD-induced exon in the HEXA gene using RNA sequencing is shown visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the HEXA gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr15 72356652 72375719 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 52]

[0087] Figure 52 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the HEXA gene. Identification of an NMD-induced exon in the HEXA gene using RNA sequencing is shown visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the HEXA gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr15 72345552 72346234 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 53]

[0088] Figure 53 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the NR1H4 gene. Identification of an NMD-induced exon in the NR1H4 gene using RNA sequencing is visualized and shown in the UCSC genome browser. The top panel shows a scaled graphical representation of the NR1H4 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr12 100493403 100505574 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 54]

[0089] Figure 54 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the STK11 gene. Identification of an NMD-induced exon in the STK11 gene using RNA sequencing is visualized and shown in the UCSC genome browser. The top panel shows a scaled graphical representation of the STK11 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr19 1207204 1218416 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 55]

[0090] Figure 55 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the STK11 gene. Identification of an NMD-induced exon in the STK11 gene using RNA sequencing is shown visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the STK11 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr19 1221341 1221948 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 56]

[0091] Figure 56 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the PCCA gene. Identification of an NMD-induced exon in the PCCA gene using RNA sequencing is shown visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the PCCA gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr13 100302999 100307191 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 57]

[0092] Figure 57 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the MUT gene. Identification of an NMD-induced exon in the MUT gene using RNA sequencing is shown visualized in the UCSC genome browser. The top panel shows a scaled graphical representation of the MUT gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr6 49435625 49440205 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 58]

[0093] Figure 58 shows the identification of an exemplary nonsense-mediated mRNA decay (NMD)-induced exon in the OPA1 gene. Identification of an NMD-induced exon in the OPA1 gene using RNA sequencing is visualized and shown in the UCSC genome browser. The top panel shows a scaled graphical representation of the OPA1 gene. Peaks corresponding to RNA sequencing reads were identified in the intron GRCh38 / hg38:chr3 193593374 193614710 shown in the middle panel. Bioinformatics analysis identified an exon-like sequence (bottom panel, sequence highlighted in capital letters) flanked by 3' and 5' splice sites. Inclusion of this exon results in the introduction of a premature stop codon, making the transcript a target for NMD. [Figure 59]

[0094] Figure 59 shows confirmation of NMD-induced exons via puromycin or cycloheximide treatment in various cell lines. RT-PCR analysis using total RNA from water-treated, DMSO-treated, puromycin-treated, or cycloheximide-treated cells confirmed the presence of a band corresponding to the NMD-induced exon 8x (GRCh38 / hg38:chr1 243564285 243564388) of the AKT3 gene. [Figure 60]

[0095] Figure 60 shows an exemplary ASO walk centered on the AKT3 exon 8x (GRCh38 / hg38:chr1 243564285 243564388) region. A graphic representation of ASO walks was performed centered on the AKT3 exon 8x (GRCh38 / hg38:chr1 243564285 243564388) region, targeting sequences upstream of the 3' splice site, across the 3' splice site, exon 8x, across the 5' splice site, and downstream of the 5' splice site. ASOs were designed to cover these regions by moving five nucleotides at a time. [Figure 61]

[0096] Figure 61 shows the AKT3 exon 8x (GRCh38 / hg38:chr1 243564285 243564388) region ASO walking assessed by reverse transcription Taqman-qPCR. A graph of the fold change in AKT3-generated mRNA product compared to Sham is plotted. [Figure 62]

[0097] Figure 62 shows confirmation of NMD-induced exons via cycloheximide treatment in various cell lines. RT-PCR analysis using total RNA from DMSO-treated or cycloheximide-treated cells confirmed the presence of a band corresponding to the NMD-induced exon 14x (GRCh38 / hg38:chr13 100305751 100305834) of the PCCA gene. [Figure 63]

[0098] Figure 63 shows an exemplary ASO walk centered on the PCCA exon 14x (GRCh38 / hg38:chr13 100305751 100305834) region. A graphic representation of ASO walks was performed centered on the PCCA exon 14x (GRCh38 / hg38:chr13 100305751 100305834) region, targeting sequences upstream of the 3' splice site, across the 3' splice site, exon 14x, across the 5' splice site, and downstream of the 5' splice site. ASOs were designed to cover these regions by moving five nucleotides at a time. [Figure 64]

[0099] Figure 64 shows the PCCA exon 14x (GRCh38 / hg38:chr13 100305751 100305834) region ASO walking assessed by reverse transcription Taqman-qPCR and RT-PCR. Graphs of the fold change in PCCA-generated mRNA product (gray) and the percentage change in NMD exon inclusion (black) compared to Sham are plotted. [Figure 65]

[0100] Figure 65 shows confirmation of NMD-induced exons via puromycin or cycloheximide treatment in various cell lines, as well as confirmation of NMD-induced exons in brain and retina samples. RT-PCR analysis using total RNA from water-, DMSO-, puromycin-, or cycloheximide-treated cells confirmed the presence of a band corresponding to the NMD-induced exon 7x (GRCh38 / hg38:chr3 193628509 193628616) of the OPA1 gene. [Figure 66]

[0101] Figure 66 shows an exemplary ASO walk centered on the OPA1 exon 7x (GRCh38 / hg38:chr3 193628509 193628616) region. A graphic representation of an ASO walk centered on the OPA1 exon 7x (GRCh38 / hg38:chr3 193628509 193628616) region was performed, targeting sequences upstream of the 3' splice site, across the 3' splice site, exon 7x, across the 5' splice site, and downstream of the 5' splice site. ASOs were designed to cover these regions by moving five nucleotides at a time, or three nucleotides when crossing the splice site region. [Figure 67]

[0102] Figure 67 shows OPA1 exon 7x (GRCh38 / hg38:chr3 193628509 193628616) region ASO walking assessed by Taqman RT-qPCR. A graph of the fold change in OPA1-generated mRNA product compared to Sham is plotted. [Figure 68]Figure 68 shows OPA1 exon 7x (GRCh38 / hg38:chr3 193628509 193628616) region ASO walking assessed by Taqman RT-qPCR. A graph of the fold change in OPA1-generated mRNA product compared to Sham is plotted. [Figure 69]

[0103] Figure 69 shows confirmation of NMD-induced exons via cycloheximide treatment in ReNCell VM and the presence of NMD-induced exon mRNA (NF1) in both human and monkey cortex. RT-PCR analysis using total RNA from DMSO- or cycloheximide-treated cells confirmed the presence of a band corresponding to the NMD-induced exon 31x (GRCh38 / hg38:chr17 31249955 31250125) of the NF1 gene. [Figure 70]

[0104] Figure 70 shows an exemplary ASO walk centered on the NF1 exon 31x (GRCh38 / hg38:chr17 31249955 31250125) region. A graphic representation of ASO walks centered on the NF1 exon 31x (GRCh38 / hg38:chr17 31249955 31250125) region was performed, targeting sequences upstream of the 3' splice site, across the 3' splice site, exon 31x, across the 5' splice site, and downstream of the 5' splice site. ASOs were designed to cover these regions by moving five nucleotides at a time. [Figure 71]

[0105] Figure 71 shows the NF1 exon 31x (GRCh38 / hg38:chr17 31249955 31250125) region ASO walking assessed by RT-PCR (top) and RT-TaqMan-qPCR (bottom). RT-PCR results indicating loss of exon 31x are shown, along with a graph of the fold change in NF1-generated mRNA product compared to sham. [Figure 72]

[0106] Figure 72 shows confirmation of NMD-induced exons via puromycin or cycloheximide treatment in various cell lines. RT-PCR analysis using total RNA from water-treated, DMSO-treated, puromycin-treated, or cycloheximide-treated cells confirmed the presence of a band corresponding to the NMD-induced exon 18x (GRCh38 / hg38:chr6 33448789 33448868) of the SYNGAP1 gene. [Figure 73]

[0107] Figure 73 shows an exemplary ASO walk centered on the SYNGAP1 exon 18x (GRCh38 / hg38:chr6 33448789 33448868) region. A graphic representation of an ASO walk centered on the SYNGAP1 exon 18x (GRCh38 / hg38:chr6 33448789 33448868) region was performed, targeting sequences upstream of the 3' splice site, across the 3' splice site, exon 18x, across the 5' splice site, and downstream of the 5' splice site. ASOs were designed to cover these regions by moving five nucleotides at a time. [Figure 74]

[0108] Figure 74 shows the SYNGAP1 exon 18x (GRCh38 / hg38:chr6 33448789 33448868) region ASO walking assessed by RT-PCR (top) and RT-TaqMan-qPCR (bottom). Graphs of exon 18x inclusion percentage and fold change in SYNGAP1-generated mRNA product compared to sham are plotted (top and bottom, respectively). [Figure 75]

[0109] Figure 75 shows confirmation of NMD-induced exon 30x via cycloheximide treatment. RT-PCR analysis using total RNA from DMSO-treated or cycloheximide-treated cells confirmed the presence of a band corresponding to the NMD-induced exon 30x (GRCh38 / hg38:chr15 92998149 92998261) of the CHD2 gene. Also shown is RT-PCR analysis demonstrating the presence of mRNA containing the NMD-induced exon 30x in cortical samples from mice, non-human primates, and humans. [Figure 76]

[0110] Figure 76 shows an exemplary ASO walk centered on the CHD2 exon 30x (GRCh38 / hg38:chr15 92998149 92998261) region. A graphic representation of ASO walks was performed centered on the CHD2 exon 30x (GRCh38 / hg38:chr15 92998149 92998261) region, targeting sequences upstream of the 3' splice site, across the 3' splice site, exon 30x, across the 5' splice site, and downstream of the 5' splice site. ASOs were designed to cover these regions by moving five nucleotides at a time. [Figure 77]

[0111] Figure 77 shows the CHD2 exon 30x (GRCh38 / hg38:chr15 92998149 92998261) region ASO walking assessed by RT-PCR. RT-PCR results demonstrating changes in the amount of mRNA containing NMD-induced exon 30x are shown. [Figure 78]

[0112] Figure 78 shows the changes in the levels of CHD2 non-producing exon (exon 30x (GRCh38 / hg38:chr15 92998149 92998261)) and CHD2-producing mRNA induced by different ASOs. DETAILED DESCRIPTION OF THE INVENTION

[0032]

[0113] ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, G ALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, P RPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR Alternative splicing events in the 1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 genes can result in nonproductive mRNA transcripts that can lead to abnormal protein expression, and are associated with the development of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, C OL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, N SD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, T Therapeutic agents that can target alternative splicing events in the OPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 genes can regulate functional protein expression levels and / or inhibit abnormal protein expression in patients with DS.Such therapeutic agents include ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RA It can be used to treat conditions caused by deficiencies of I1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 proteins.

[0033]

[0114] One alternative splicing event that can result in a non-productive mRNA transcript is the inclusion of an additional exon in the mRNA transcript that can induce nonsense-mediated mRNA decay. The present disclosure relates to the following genes: ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL , NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC2 5A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA It regulates alternative splicing of 3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 to enhance the protein-coding mature mRNA and, therefore, the translated functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF Compositions and methods are provided for increasing production of 1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein.These compositions and methods cause exon skipping, e.g., pseudo-exon skipping, and are useful in treating the inflammatory bowel disease caused by ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN , PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 antisense oligomers (ASOs) capable of promoting constitutive splicing of pre-mRNA.In various embodiments, functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1 , OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, S PTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN 1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein may be increased using the methods of the present disclosure to enhance the expression of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, R AI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL. Conditions caused by 11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein deficiencies can be treated. Splicing and nonsense-mediated mRNA decay

[0115] Intervening sequences, or introns, are removed by a large, highly dynamic RNA-protein complex called the spliceosome, which orchestrates complex interactions between the primary transcript, small nuclear RNAs (snRNAs), and numerous proteins. The spliceosome assembles in an orderly fashion on each intron, starting with recognition of the 5' splice site (5'ss) by U1 snRNA or the 3' splice site (3'ss) by the U2 pathway, which is responsible for binding of the U2 accessory factor (U2AF) to the 3'ss region, facilitating U2 binding to the branch point sequence (BPS). U2AF is a stable heterodimer composed of a 65 kD subunit (U2AF65) encoded by U2AF2, which binds the polypyrimidine tract (PPT), and a 35 kD subunit (U2AF35) encoded by U2AF1, which interacts with the highly conserved AG dinucleotide in the 3'ss, stabilizing U2AF65 binding. In addition to the BPS / PPT unit and 3'ss / 5'ss, accurate splicing requires auxiliary sequences or structures known as intron or exon splicing enhancers or silencers that activate or repress splice site recognition. These elements enable true splice sites to be recognized from the vast excess of cryptic or pseudosites in the genomes of higher eukaryotes, which have the same sequence but are 10-fold more abundant than true sites. Although elements often have regulatory functions, the precise mechanisms of their activation or repression are not fully understood.

[0034]

[0116] The decision to splice or not can typically be modeled as a stochastic rather than a deterministic process, as even the most well-defined splicing signals can occasionally be misspliced. However, under normal conditions, pre-mRNA splicing occurs with surprisingly high fidelity. This is thought to be due, in part, to the activity of adjacent cis-acting auxiliary exon and intron splicing control elements (ESRs or ISRs). These functional elements are typically classified as either exon or intron splicing enhancers (ESEs or ISEs) or silencers (ESSs or ISSs) based on their ability to stimulate or inhibit splicing, respectively. Although there is now evidence that some auxiliary cis-acting elements can act by influencing the dynamics of spliceosome assembly, for example, by affecting the positioning of the complex between the U1 snRNP and the 5'ss, it seems highly likely that many elements function in concert with trans-acting RNA-binding proteins (RBPs). For example, the serine- and arginine-rich family of RBPs (SR proteins) is a conserved family of proteins that play a key role in defining exons. SR proteins promote exon recognition by recruiting components of the pre-spliceosome to adjacent splice sites or by attenuating the effect of ESSs in their vicinity. The repressive effect of ESSs can be mediated by members of the heterogeneous nuclear ribonucleoprotein (hnRNP) family, which can alter the recruitment of core splicing factors to adjacent splice sites. In addition to their role in splicing control, silencer elements have been suggested to play a role in suppressing pseudoexons, which are sets of decoy intron splice sites that have the typical spacing of an exon but lack a functional open reading frame. ESEs and ESSs, along with their cognate trans-acting RBPs, represent key components in a set of splicing control factors that specify how, where, and when mRNA is assembled from its precursor.

[0035]

[0117] Sequences marking exon-intron boundaries are degenerate signals of varying strength that occur frequently within human genes. In multi-exon genes, different pairs of splice sites can be joined together in many different combinations to generate a wide variety of transcripts from a single gene. This is commonly referred to as alternative pre-mRNA splicing. Although most mRNA isoforms produced by alternative splicing can be exported from the nucleus and translated into functional polypeptides, different mRNA isoforms derived from a single gene can vary greatly in their translation efficiency. mRNA isoforms that contain a premature termination codon (PTC) at least 50 bp upstream of the exon junction complex are likely to be targeted for degradation by the nonsense-mediated mRNA decay (NMD) pathway. Mutations in traditional (BPS / PPT / 3'ss / 5'ss) and auxiliary splicing motifs can cause aberrant splicing, such as exon skipping, or cryptic (or false) exon inclusion or splice site activation, and can be a significant contributor to human morbidity and mortality. Both aberrant and alternative splicing patterns can be influenced by natural DNA variants in exons and introns.

[0036]

[0118] Considering that exon-intron boundaries can occur at any of three codon positions, it is clear that only a subset of alternative splicing events can maintain the standard open reading frame. For example, only exons divisible by three can be skipped or included in the mRNA without any change in the reading frame. Splicing events that are not in phase with one another can induce frameshifts. Unless reversed by downstream events, frameshifts inevitably result in one or more PTCs, likely resulting in their subsequent degradation by NMD. NMD is a translation-coupled mechanism that eliminates mRNAs containing PTCs. NMD can function as a surveillance pathway present in all eukaryotes. NMD can reduce errors in gene expression by eliminating mRNA transcripts containing premature stop codons. Translation of these aberrant mRNAs can potentially result in harmful gain-of-function or blockade of function in the resulting proteins. NMD targets not only transcripts with PTCs but also a wide range of mRNA isoforms expressed from many endogenous genes, suggesting that NMD is a master regulator driving both fine and coarse regulation of steady-state RNA levels in cells.

[0037]

[0119] An NMD-inducing exon (NIE) is a pseudoexon, a region within an exon or intron, that can activate the NMD pathway when included in a mature RNA transcript. In constitutive splicing events, the intron containing the NIE is typically excised, but during alternative or aberrant splicing events, the intron or a portion thereof (e.g., the NIE) may be retained. Mature mRNA transcripts containing such NIEs may be non-productive due to a frameshift that induces the NMD pathway. The inclusion of an NIE in a mature RNA transcript can downregulate gene expression. An mRNA transcript containing an NIE may be referred to in the present disclosure as an "NIE-containing mRNA" or "NMD exon mRNA."

[0038]

[0120] Cryptic (or false splice sites) have the same splicing recognition sequence as true splice sites but are not used in the splicing reaction. They are 10 times more abundant than true splice sites in the human genome and are usually suppressed by molecular mechanisms that are not yet fully understood. Cryptic 5' splice sites have the consensus NNN / GUNNNN or NNN / GCNNNN, where N is any nucleotide and / is the exon-intron boundary. Cryptic 3' splice sites have the consensus NAG / N. Activation of these splice sites involves reversing them to the optimal consensus of the original splice site, i.e., MAG / GURAGU and YAG, respectively. The nucleotide sequence is positively affected by the surrounding nucleotides making it more similar to / G, where M is C or A, R is G or A, and Y is C or U.

[0039]

[0121] Splice sites and their regulatory sequences can be identified by those skilled in the art, for example, in Kralovicova, J. and Vorechovsky, I. (2007) Global control of aberrant splice site activation by auxiliary splicing sequences: evidence for a gradient in exon and intron definition. Nucleic Acids Res., 35, 6399-6413 (http: / / www.ncbi.nlm.nih.gov / pmc / articles / PMC2095810 / pdf / gkm680.pdf) can be readily identified using suitable publicly available algorithms.

[0040]

[0122] Cryptic splice sites or splicing control sequences may compete with the splice site of the NIE for RNA-binding proteins such as U2AF. In some embodiments, an agent may bind to a cryptic splice site or splicing control sequence and prevent binding of the RNA-binding protein, thereby favoring binding of the RNA-binding protein to the NIE splice site.

[0041]

[0123] In some embodiments, the cryptic splice site may not include the 5' or 3' splice site of the NIE. In some embodiments, the cryptic splice site may be at least 10 nucleotides, at least 20 nucleotides, at least 50 nucleotides, at least 100 nucleotides, or at least 200 nucleotides upstream of the NIE 5' splice site. In some embodiments, the cryptic splice site may be at least 10 nucleotides, at least 20 nucleotides, at least 50 nucleotides, at least 100 nucleotides, or at least 200 nucleotides downstream of the NIE 3' splice site. Target transcript

[0124] In some embodiments, the methods of the disclosure comprise the steps of: ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, P We exploit the presence of NIEs in pre-mRNAs transcribed from the RPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 genes. Functional maturation ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4 , DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, M UT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNA Identified ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, and NF1 mRNAs. , PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 NIESplicing of pre-mRNA species can be induced using therapeutic agents such as ASOs that stimulate exon skipping of NIEs. Induction of exon skipping can result in inhibition of the NMD pathway. The resulting mature mRNAs include ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PL CB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, C D46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1The mRNA is usually translated without activating the NMD pathway, thereby increasing the expression of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, and NF-kappaB1 in patient cells. MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHA NK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C , SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein levels, and ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, G RN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, R AI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A Conditions or diseases associated with deficiencies of CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1, such as Alport syndrome; amyotrophic lateral sclerosis (ALS); Angelman syndrome; primary progressive aphasia; arrhythmogenic right ventricular dysplasia (RDC); autism spectrum disorder; dilated cardiomyopathy (DCM); myofibrillar myopathy (MM); neuronal ceroid lipofuscinosis (CERI); intrahepatic cholestasis of pregnancy (ICP); progressive familial intrahepatic cholestasis (ICH); citrullinemia type II; citrullinemia type 1; with or without cerebral ataxia. Cognitive impairment; Cornelia de Lange; Early-onset epileptic encephalopathy; Epilepsy-aphasia spectrum disorder; Generalized epilepsy with febrile convulsions plus type 7; Childhood-onset epileptic encephalopathy; Early infantile epileptic encephalopathy type 11; Early infantile epileptic encephalopathy type 12; Early infantile epileptic encephalopathy type 13; Early infantile epileptic encephalopathy type 2; Paroxysmal ataxia type 2; Familial focal epilepsy; Familial febrile convulsions type 3B; Friedreich's ataxia; Friedreich's ataxia with preserved reflexes; Galactose epimerase deficiency; Primary congenital glaucoma type 3E; Glycogen storage disease type IV; GRN-related frontotemporal dementia; B6-responsive and non-responsive homocystinuria; Autosomal recessive HSAN2D; Congenital insensitivity to pain; Kabuki syndrome; Koolen-De Vries Vries syndrome; autosomal dominant mental retardation 1; methylmalonic aciduria; familial hemiplegic migraine 1; myoclonic atonic epilepsy; neurofibromatosis type 1; opioid dependence; optic atrophy type 1; Phelan-McDermid syndrome; propionic acidemia; primary open-angle glaucoma; propionic acidemia; retinitis pigmentosa 11; retinitis pigmentosa 18; retinitis pigmentosa 31; retinitis pigmentosa 59; Rett syndrome; benign familial infantile seizures 3; benign familial infantile seizures 5; Smith-Magenis syndrome; Sotos syndrome 1; Beckwith-Wiedemann syndrome; Stargardt disease 3; Tay-Sachs disease; tuberous sclerosis complex; tyrosinemia type 1; Wagner syndrome 1; West syndrome; Wolfram syndrome 2 / NAFLD; 15q13.3 microdeletion; 16p11.It can alleviate symptoms of 2 deletion syndrome; autosomal dominant hearing loss 13; cone-rod retinal dystrophy 2; autosomal dominant hearing loss 4A; peripheral neuropathy, myopathy, hoarseness, and hearing loss; autosomal dominant hearing loss 22; neurofibromatosis type 2; NASH; or autosomal dominant mental retardation 5.

[0042]

[0125] In some embodiments, diseases or conditions that can be treated or ameliorated using the methods or compositions disclosed herein are not directly related to the target protein (gene) targeted by the therapeutic agent. In some embodiments, the therapeutic agents provided herein may target a protein (gene) that is not directly related to the disease or condition, but can treat or ameliorate the disease or condition by modulating the expression of that target protein (gene). For example, the therapeutic agents provided herein can treat or ameliorate ocular diseases or conditions by targeting genes such as CD46, CFH, CR1, DNAJC8, EIF2AK3, ERN1, GUCY2F, GUCY2F, SEMA3C, SEMA3D, SIRT3, or AKT3. In some embodiments, targeting genes CD46, CFH, CR1, DNAJC8, EIF2AK3, ERN1, GUCY2F, GUCY2F, SEMA3C, SEMA3D, SIRT3, or AKT3 is said to be indicated for the ocular pathway. In some embodiments, targeting a gene such as SCN8A can treat or ameliorate a central nervous system disorder, such as epilepsy, e.g., Dravet syndrome. In some embodiments, a target gene such as SCN8A is said to be indicative of a pathway (central nervous system) or pathway (central nervous system, epilepsy).

[0043]

[0126] In various embodiments, the present disclosure provides methods for detecting and / or treating a variety of conditions, including ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUTherapeutic agents are provided that target T, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 mRNA transcripts and regulate splicing or protein expression levels. The therapeutic agents can be small molecules, polynucleotides, or polypeptides. In some embodiments, the therapeutic agent is an ASO. ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, P Various regions or sequences of RPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 pre-mRNA can be targeted by therapeutic agents, e.g., ASOs.In some embodiments, the ASO contains an NIE: ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB , PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 mRNA precursor transcripts. In some embodiments, the ASO is selected from the group consisting of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP 2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 target sequences within the NIE of the mRNA precursor transcript.In some embodiments, the ASO is ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDD. S, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NI PBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, S Targets sequences upstream (or 5'-side) from the 5' end (3'ss) of the NIE of HANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 mRNA precursor transcripts. In some embodiments, the ASO is selected from the group consisting of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP 2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 mRNA precursor transcripts, targeting sequences downstream (or 3' to) the NIE (protein-independent inhibitor) 3' end (5' ss) of the precursor transcript.In some embodiments, the ASO is selected from the group consisting of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2 , PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1. In some embodiments, the ASO targets a sequence within the intron adjacent to the 5' end of the NIE of the pre-mRNA transcript. In some embodiments, the ASO targets a sequence within the intron adjacent to the 5' end of the NIE of the pre-mRNA transcript. In some embodiments, the ASO targets a sequence within the intron adjacent to the 5' end of the NIE of the pre-mRNA transcript. In some embodiments, the ASO targets a sequence within the intron adjacent to the 5' end of the NIE of the pre-mRNA transcript. In some embodiments, the ASO targets a sequence within the intron adjacent to the In some embodiments, the ASO targets sequences within the intron adjacent to the 3' end of the NIE of the 2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 pre-mRNA transcript. ACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, The target sequence includes the NIE-intron boundary of the RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 mRNA precursor transcript. The NIE-intron boundary may refer to the junction between the intron sequence and the NIE region. The intron sequence may be adjacent to the 5' end of the NIE or the 3' end of the NIE. In some embodiments, the ASO is selected from the group consisting of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5 , MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX , DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 mRNA precursor transcripts. In some embodiments, the ASO is selected from the group consisting of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP 2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 target sequences within introns of the mRNA precursor transcript. In some embodiments, the ASO is selected from the group consisting of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5 , MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CR. The target sequence includes both a portion of an intron and a portion of an exon of the X, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 pre-mRNA transcript.

[0044]

[0127] In some embodiments, the ASO targets a sequence about 4 to about 300 nucleotides upstream (or 5') from the 5' end of the NIE. In some embodiments, the ASO targets a sequence about 1 to about 20 nucleotides, about 20 to about 50 nucleotides, about 50 to about 100 nucleotides, about 100 to about 150 nucleotides, about 150 to about 200 nucleotides, about 200 to about 250 nucleotides, or about 250 to about 300 nucleotides upstream (or 5') from the 5' end of the NIE region. In some embodiments, the ASO may target a sequence more than 300 nucleotides upstream from the 5' end of the NIE. In some embodiments, the ASO targets a sequence about 4 to about 300 nucleotides downstream (or 3') from the 3' end of the NIE. In some embodiments, the ASO targets a sequence about 1 to about 20 nucleotides, about 20 to about 50 nucleotides, about 50 to about 100 nucleotides, about 100 to about 150 nucleotides, about 150 to about 200 nucleotides, about 200 to about 250 nucleotides, or about 250 to about 300 nucleotides downstream from the 3' end of the NIE. In some embodiments, the ASO targets a sequence more than 300 nucleotides downstream from the 3' end of the NIE.

[0045]

[0128] In some embodiments, the inhibitors of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, P LCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, C D46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 The NIE-containing pre-mRNA transcript is encoded by a gene sequence having at least about 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 1-59 or 192-211.In some embodiments, the inhibitors of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, P The LCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 NIE mRNA precursor transcript comprises a sequence having at least about 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs:60-191.

[0046]

[0129] In some embodiments, the inhibitors of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, P LCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 NIE-containing precursor mRNA transcripts (or NMD exon mRNAs) comprise a sequence having at least about 80%, 85%, 90%, 95%, 97%, or 100% sequence identity to any one of SEQ ID NOs: 60-191.In some embodiments, the inhibitors of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, P LCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 NIE-containing precursor mRNA transcripts (or NMD exon mRNAs) are encoded by a sequence having at least about 80%, 85%, 90%, 95%, 97%, or 100% sequence identity to any one of SEQ ID NOs: 60-191. In some embodiments, the targeted portion of the NMD exon mRNA comprises a sequence having at least 80%, 85%, 90%, 95%, 97%, or 100% sequence identity to a region comprising at least 8 consecutive nucleic acids of any one of SEQ ID NOs: 60-191.

[0047]

[0130] In some embodiments, the ASO comprises exon 8x of ABCB4 NIE-containing pre-mRNA comprising NIE exon 8, exon 9x of ASS1 NIE-containing pre-mRNA comprising NIE exon 9, exon 16x of ATP8B1 NIE-containing pre-mRNA comprising NIE exon 16, exon 1x of BAG3 NIE-containing pre-mRNA comprising NIE exon 1, exon 31x of CACNA1A NIE-containing pre-mRNA comprising NIE exon 31, exon 36x of CACNA1A NIE-containing pre-mRNA comprising NIE exon 36, exon 37x of CACNA1A NIE-containing pre-mRNA comprising NIE exon 37, exon 3x of CBS NIE-containing pre-mRNA comprising NIE exon 3, exon 12x of CBS NIE-containing pre-mRNA comprising NIE exon 12, exon 1x of CD55 NIE-containing pre-mRNA comprising NIE exon 1, and CDKL5 CFH, containing exon 16x of NIE-containing pre-mRNA and NIE exon 3 CHD2, containing exon 3x of NIE-containing pre-mRNA and NIE exon 30 CHRNA7, containing exon 4x of NIE-containing pre-mRNA and NIE exon 1 CISD2, containing exon 1x of NIE-containing pre-mRNA and NIE exon 15 CLN3, containing exon 15x of NIE-containing pre-mRNA and NIE exon 11 COL4A3, containing exon 11x of NIE-containing pre-mRNA and NIE exon 41 CO L4A3 contains exon 41x of NIE-containing pre-mRNA and NIE exon 22 COL4A4 contains exon 22x of NIE-containing pre-mRNA and NIE exon 44 COL4A4 contains exon 44x of NIE-containing pre-mRNA and NIE exon 20 DEPDC5 contains exon 20x of NIE-containing pre-mRNA and NIE exon 2 DHDDS contains exon 2x of NIE-containing pre-mRNA and NIE exon 3 ELOVL4 contains exon 2x of NIE-containing pre-mRNA and NIE exon 3 Exon 3x of NIE-containing pre-mRNA, exon 5x of FAH NIE-containing pre-mRNA containing NIE exon 5, exon 4x of FXN NIE-containing pre-mRNA containing NIE exon 4, exon 4x of GALE NIE-containing pre-mRNA containing NIE exon 4, exon 3x of GBE1 NIE-containing pre-mRNA containing NIE exon 3, exon 11x of GRIN2A NIE-containing pre-mRNA containing NIE exon 11, exon 1x of GRN NIE-containing pre-mRNA containing NIE exon 1, exon 2x of HEXA NIE-containing pre-mRNA containing NIE exon 2, exon 2x of KANSL1 NIE-containing pre-mRNA containing NIE exon 2, exon 1x of KCNQ2 NIE-containing pre-mRNA containing NIE exon 1, exon 50x of KMT2D NIE-containing pre-mRNA containing NIE exon 50, exon 8 of MAPK3 MBD5 contains exon 8x of the NIE-containing pre-mRNA and NIE exon 13. MECP2 contains exon 13x of the NIE-containing pre-mRNA and NIE exon 2. MUT contains exon 2x of the NIE-containing pre-mRNA and NIE exon 11. NF1 contains exon 11x of the NIE-containing pre-mRNA and NIE exon 31. NIPBL contains exon 7x of the NIE-containing pre-mRNA and NIE exon 38. NSD1 contains exon 11x of the NIE-containing pre-mRNA and NIE exon 6. OPA1 contains exon 6x of the NIE-containing pre-mRNA and NIE exon 28. OPA1 contains exon 28x of the NIE-containing pre-mRNA and NIE exon 1. OPTN contains exon 1x of the NIE-containing pre-mRNA and NIE exon 1. PCCA contains exon 1. NIE-containing pre-mRNA exon 1x, PCCB NIE-containing pre-mRNA exon 5x, PCCB NIE-containing pre-mRNA exon 6x, PKP2 NIE-containing pre-mRNA exon 4x, PLCB1 NIE-containing pre-mRNA exon 23x, PRPF3 NIE-containing exon 3exon 3x of NIE-containing pre-mRNA, PRPF31 containing exon 9, exon 9x of NIE-containing pre-mRNA, RAI1 containing exon 1, exon 1x of NIE-containing pre-mRNA, RBFOX2 containing exon 5, exon 5x of NIE-containing pre-mRNA, SCN2A containing exon 13, exon 13x of NIE-containing pre-mRNA, SCN3A containing exon 6x of NIE-containing pre-mRNA, SCN3A containing exon 7, exon 4x of NIE-containing pre-mRNA, SCN8A containing exon 4, exon 6x of NIE-containing pre-mRNA, SCN8A containing exon 20, exon 20x of NIE-containing pre-mRNA, SCN9A containing exon 6, SHANK3 containing exon 24 SLC25A13 containing exon 24x of NIE-containing pre-mRNA, exon 3 of NIE-containing pre-mRNA, exon 3 of NIE-containing pre-mRNA, SLC25A13 containing exon 6 of NIE-containing pre-mRNA, exon 6x of NIE-containing pre-mRNA, SLC25A13 containing exon 9 of NIE-containing pre-mRNA, exon 9x of NIE-containing pre-mRNA, SLC25A13 containing exon 11 of NIE-containing pre-mRNA, SLC25A13 containing exon 11x of NIE-containing pre-mRNA, SLC25A13 containing exon 13x of NIE-containing pre-mRNA, SLC6A1 containing exon 1x of NIE-containing pre-mRNA, exon 12 of NIE-containing pre-mRNA, SLC6A1 containing exon 12 of NIE-containing pre-mRNA, SLC6A1 containing exon 12 of NIE-containing pre-mRNA, SLC6A1 containing exon 12 of NIE-containing pre-mRNA, TEK containing exon 10x of NIE-containing pre-mRNA, TEK containing exon 15x of NIE-containing pre-mRNA, NIE exon 1 exon 1x of TOPORS NIE-containing pre-mRNA, exon 11x of TSC2 NIE-containing pre-mRNA containing NIE exon 11, exon 30x of TSC2 NIE-containing pre-mRNA containing NIE exon 30, exon 1x of UBE3A NIE-containing pre-mRNA containing NIE exon 1, or exon 7x of VCAN NIE-containing pre-mRNA containing NIE exon 7. In some embodiments, the ASO targets exons of AKT3 (GRCh38 / hg38:chr1 243564285 243564388); exons of CBS (GRCh38 / hg38:chr21 43059730 43060012); exons of CD46 (GRCh38 / hg38:chr1 207775610 207775745); exons of CFH (GRCh38 / hg38:chr1 196675450 196675529); exons of CHD2 (GRCh38 / hg38:chr15 92998149 92998261); exons of CLN3 (GRCh38 / hg38:chr16 28479644 28479765); exons of COL11A2 (GRCh38 / hg38:chr6 COL4A3 exons (GRCh38 / hg38:chr2 227296487 227296526); COL4A4 exons (GRCh38 / hg38:chr2 227144653 227144833); COL4A4 exons (GRCh38 / hg38:chr2 227015283 227015360); CR1 exons (GRCh38 / hg38:chr1 207637688 207637848); CRX exons (GRCh38 / hg38:chr19 47835403 47835579); CYP2J2 exons (GRCh38 / hg38:chr1 59904366 59904516; DHDDS exons (GRCh38 / hg38:chr1 26442335 26442372); DNAJC8 exons (GRCh38 / hg38:chr1 28230131 28230252); EIF2AK3 exons (GRCh38 / hg38:chr2 88582755 88582824); ERN1 exons (GRCh38 / hg38:chr17 64102673 64102804); GALE exons (GRCh38 / hg38:chr1 23798311 23798484); GUCY2F exons (GRCh38 / hg38:chrX 109383365 109383446); exon of GUCY2F (GRCh38 / hg38:chrX 109439038 109439175); HEXA exon (GRCh38 / hg38:chr15 72362376 72362466); HEXA exon (GRCh38 / hg38:chr15 72345677 72345776); MAPK3 exon (GRCh38 / hg38:chr16 30115595 30115645); MBD5 exon (GRCh38 / hg38:chr2 148460219 148460304); MBD5 exon (GRCh38 / hg38:chr2 148490695 148490787); MBD5 exon (GRCh38 / hg38:chr2 148505761 148505830; MUT exon (GRCh38 / hg38:chr6 49436522 49436597); MYH14 exon (GRCh38 / hg38:chr19 50230825 50230999); MYO6 exon (GRCh38 / hg38:chr6 75867431 75867523); NF1 exon (GRCh38 / hg38:chr17 31249955 31250125); NF2 exon (GRCh38 / hg38:chr22 29628658 29628773); NIPBL exon (GRCh38 / hg38:chr5 37048127 37048354); exon of NR1H4 (GRCh38 / hg38:chr12 100499841 100500024); exon of NSD1 (GRCh38 / hg38:chr5 177169394 177169559); exon of NSD1 (GRCh38 / hg38:chr5 177200761 177200783); exon of NSD1 (GRCh38 / hg38:chr5 177247924 177248079); exon of NSD1 (GRCh38 / hg38:chr5 177 275947 177276101); OPA1 exon (GRCh38 / hg38:chr3 193628509 193628616); OPA1 exon (GRCh38 / hg38:chr3 193603500 193603557); PCCA exon (GRCh38 / hg38:chr13 100305751 100305834); PKP2 exon (GRCh38 / hg38:chr12 32894516 32894778); PPARA exon (GRCh38 / hg38:chr22 46203575 46203752); PRPF3 exon (GRCh38 / hg38:chr1 150327557 150327652); exons of PRPF3 (GRCh38 / hg38:chr1 150330401 150330498); exons of SCN2A (GRCh38 / hg38:chr2 165327155 165327202); exons of SCN8A (GRCh38 / hg38:chr12 5168875 8 51688849); exon of SCN8A (GRCh38 / hg38:chr12 51780202 51780271); exons of SCN9A (GRCh38 / hg38:chr2 166304238 166304329); exons of SEMA3C (GRCh38 / hg38:chr7 80794854 80794957); exons of SEMA3D (GRCh38 / hg38:chr7 85059498 85059541); exons of SIRT3 (GRCh38 / hg38:chr11 225673 226081); exons of STK11 (GRCh38 / hg38:chr19 1216268 1216398); exons of STK11 (GRCh38 / hg38:chr19 1221621 1221846); exons of SYNGAP1 (GRCh38 / hg38:chr6 33448789 33448868); exons of TOPORS (GRCh38 / hg38:chr9 32551365 32551469); exons of VCAN (GRCh38 / hg38:chr5 83544965 83545070).

[0048]

[0131] In some embodiments, the ASO is selected from the group consisting of ABCB4 exon 8x, ASS1 exon 9x, ATP8B1 exon 16x, BAG3 exon 1x, CACNA1A exon 31x, CACNA1A exon 36x, CACNA1A exon 37x, CBS exon 3x, CBS exon 12x, CD55 exon 1x, CDKL5 exon 16x, CFH exon 3x, CHD2 exon 30x, CHRNA7 exon 4x, CISD2 exon 1x, and CLN3 exon 15x. , COL4A3 exon 11x, COL4A3 exon 41x, COL4A4 exon 22x, COL4A4 exon 44x, DEPDC5 exon 20x, DHDDS exon 2x, ELOVL4 exon 3x, FAH exon 5x, FXN exon 4x, GALE exon 4x, GBE1 exon 3x, GRIN2A exon 11x, GRN exon 1x, HEXA exon 2x, KANSL1 exon 2x, KCNQ2 exon 1x, KMT2D exon 50x, M APK3 exon 8x, MBD5 exon 13x, MECP2 exon 2x, MUT exon 11x, NF1 exon 31x, NIPBL exon 7x, NIPBL exon 38x, NSD1 exon 11x, OPA1 exon 6x, OPA1 exon 28x, OPTN exon 1x, PCCA exon 1x, PCCB exon 5x, PCCB exon 6x, PKP2 exon 4x, PLCB1 exon 23x, PRPF3 exon 3x, PRPF31 exon 9x, R AI1 exon 1x, RBFOX2 exon 5x, SCN2A exon 13x, SCN3A exon 6x, SCN3A exon 7x, SCN8A exon 4x, SCN8A exon 6x, SCN8A exon 20x, SCN9A exon 6x, SHANK3 exon 24x, SLC25A13 exon 3x, SLC25A13 exon 6x, SLC25A13 exon 9x, SLC25A13 exon 11x, SLC25A13 exon 13x, SLC6A1 exon 1x, The target sequence is approximately 1500 nucleotides, approximately 1000 nucleotides, approximately 800 nucleotides, approximately 700 nucleotides, approximately 600 nucleotides, approximately 500 nucleotides, approximately 400 nucleotides, approximately 300 nucleotides, approximately 200 nucleotides, approximately 100 nucleotides, approximately 80 nucleotides, approximately 70 nucleotides, approximately 60 nucleotides, or approximately 50 nucleotides upstream (or 5' side) of the 5' end of exon 12x of SPTAN1, exon 10x of TEK, exon 15x of TEK, exon 1x of TOPORS, exon 11x of TSC2, exon 30x of TSC2, exon 1x of UBE3A, or exon 7x of VCAN.In some embodiments, the ASO is selected from the group consisting of AKT3GRCh38 / hg38:chr1 243564388; CACNA1AGRCh38 / hg38:chr19 13236618; CBSGRCh38 / hg38:chr21 43060012; CD46GRCh38 / hg38:chr1 207775610; CFHGRCh38 / hg38:chr1 196675450; CHD2GRCh38 / hg38:chr15 92998149; CLN3GRCh38 / hg38:chr16 28479765; and COL11A2GRCh38 / hg38:chr6 33183698; COL4A3 GRCh38 / hg38:chr2 227296487; COL4A4 GRCh38 / hg38:chr2 227144833; COL4A4 GRCh38 / hg38:chr2 227015360; CR1 GRCh38 / hg38:chr1 207637688; CRX GRCh38 / hg38:chr19 47835403; CYP2J2 GRCh38 / hg38:chr1 59904516; DHDDS GRCh38 / hg38:chr1 26442335; DNAJC8 GRCh38 / hg38:chr1 28230252;EIF2AK3GRCh38 / hg38:chr2 88582824;ERN1GRCh38 / hg38:chr17 64102804;GALEGRCh38 / hg38:chr1 23798484;GUCY2FGRCh38 / hg38:chrX 109383446;GUCY2FGRCh38 / hg38:chrX 109439175;HEXAGRCh38 / hg38:chr15 72362466;HEXAGRCh38 / hg38:chr15 72345776;MAPK3GRCh38 / hg38:chr16 30115645;MBD5's GRCh38 / hg38:chr2 148460219;MBD5's GRCh38 / hg38:chr2 148490695;MBD5's GRCh38 / hg38:chr2 148505761;MUT's GRCh38 / hg38:chr6. 49436597; GRCh38 / hg38 in MYH14:chr19 50230825; GRCh38 / hg38 in MYO6:chr6 75867431; GRCh38 / hg38 in NF1:chr17 31249955; GRCh38 / hg38 in NF2:chr22 29628658; GRCh38 / hg38 in NIPBL:chr5 37048127; GRCh38 / hg38 in NR1H4:chr12 100499841; GRCh38 / hg38 in NSD1:chr5 177169394; GRCh38 / hg38 in NSD1:chr5 177200761;NSD1GRCh38 / hg38:chr5 177247924;NSD1GRCh38 / hg38:chr5 177275947;OPA1GRCh38 / hg38:chr3 193628509;OPA1GRCh38 / hg38:chr3 193603500;PCCAGRCh38 / hg38:chr13 100305751;PKP2GRCh38 / hg38:chr12 32894778;PPARAGRCh38 / hg38:chr22 46203575;PRPF3GRCh38 / hg38:chr1 150327557;PRPF3GRCh38 / hg38:chr1 150330401;SCN2AGRCh38 / hg38:chr2 165327155;SCN8AGRCh38 / hg38:chr12 51688758;SCN8AGRCh38 / hg38:chr12 51780202;SCN9AGRCh38 / hg38:chr2 166304329;SEMA3CGRCh38 / hg38:chr7 80794957;SEMA3DGRCh38 / hg38:chr7 85059541;SIRT3GRCh38 / hg38:chr11 226081;STK11 GRCh38 / The target sequences are those approximately 1500, 1000, 800, 700, 600, 500, 400, 300, 200, 100, 80, 70, 60, or 50 nucleotides upstream (or 5'-side) of hg38:chr19 1216268; GRCh38 / hg38:chr19 1221621 of STK11; GRCh38 / hg38:chr6 33448789 of SYNGAP1; GRCh38 / hg38:chr9 32551469 of TOPORS; or GRCh38 / hg38:chr5 83544965 of VCAN.

[0049]

[0132] In some embodiments, the ASO is selected from the group consisting of ABCB4 exon 8x, ASS1 exon 9x, ATP8B1 exon 16x, BAG3 exon 1x, CACNA1A exon 31x, CACNA1A exon 36x, CACNA1A exon 37x, CBS exon 3x, CBS exon 12x, CD55 exon 1x, CDKL5 exon 16x, CFH exon 3x, CHD2 exon 30x, CHRNA7 exon 4x, CISD2 exon 1x, CLN3 exon 15x, COL4A3 exon 11x, COL 4A3 exon 41x, COL4A4 exon 22x, COL4A4 exon 44x, DEPDC5 exon 20x, DHDDS exon 2x, ELOVL4 exon 3x, FAH exon 5x, FXN exon 4x, GALE exon 4x, GBE1 exon 3x, GRIN2A exon 11x, GRN exon 1x, HEXA exon 2x, KANSL1 exon 2x, KCNQ2 exon 1x, KMT2D exon 50x, MAPK3 exon 8x, MBD5 exon 13x, MECP2 exon 2x, M UT exon 11x, NF1 exon 31x, NIPBL exon 7x, NIPBL exon 38x, NSD1 exon 11x, OPA1 exon 6x, OPA1 exon 28x, OPTN exon 1x, PCCA exon 1x, PCCB exon 5x, PCCB exon 6x, PKP2 exon 4x, PLCB1 exon 23x, PRPF3 exon 3x, PRPF31 exon 9x, RAI1 exon 1x, RBFOX2 exon 5x, SCN2A exon 13x, SCN3A exon 6x, SCN3A exon exon 7x, SCN8A exon 4x, SCN8A exon 6x, SCN8A exon 20x, SCN9A exon 6x, SHANK3 exon 24x, SLC25A13 exon 3x, SLC25A13 exon 6x, SLC25A13 exon 9x, SLC25A13 exon 11x, SLC25A13 exon 13x, SLC6A1 exon 1x, SPTAN1 exon 12x, TEK exon 10x, TEK exon 15x, TOPORS exon 1x, TSC2 exon 11x, TSC2 exon 30x,In some embodiments, the ASO targets a sequence up to about 1500, 1000, 800, 700, 600, 500, 400, 300, 200, 100, 80, 70, 60, or 50 nucleotides upstream (or 5') of exon 1x of UBE3A or exon 7x of VCAN. 13236618; CBS GRCh38 / hg38:chr21 43060012; CD46 GRCh38 / hg38:chr1 207775610; CFH GRCh38 / hg38:chr1 196675450; CHD2 GRCh38 / hg38:chr15 92998149; CLN3 GRCh38 / hg38:chr16 28479765; COL11A2 GRCh38 / hg38:chr6 33183698; COL4A3 GRCh38 / hg38:chr2 227296487; COL4A4 GRCh38 / hg38:chr2 227144833;GRCh38 / hg38 in COL4A4:chr2 227015360;GRCh38 / hg38 in CR1: chr1 207637688; CRX GRCh38 / hg38:chr19 47835403; CYP2J2 GRCh38 / hg38:chr1 59904516; DHDDS GRCh38 / hg38:chr1 26442335; DNAJC8 GRCh38 / hg38:chr1 28230252; EIF2AK3 GRCh38 / hg38:chr2 88582824; ERN1 GRCh38 / hg38:chr17 64102804;GALEGRCh38 / hg38:chr1 23798484;GUCY2FGRCh38 / hg38:chrX 109383446;GUCY2FGRCh38 / hg38:chrX 109439175;HEXAGRCh38 / hg38:chr15 72362466;HEXAGRCh38 / hg38:chr15 72345776;MAPK3GRCh38 / hg38:chr16 30115645;MBD5GRCh38 / hg38:chr2 148460219;MBD5GRCh38 / hg38:chr2 148490695; MBD5 GRCh38 / hg38:chr2 148505761; MUT GRCh38 / hg38:chr6 49436597; MYH14 GRCh38 / hg38:chr19 50230825; MYO6 GRCh38 / hg38:chr6 75867431; NF1 GRCh38 / hg38:chr17 31249955; NF2 GRCh38 / hg38:chr22 29628658; NIPBL GRCh38 / hg38:chr5 37048127; NR1H4 GRCh38 / hg38:chr12 100499841; NSD1 GRCh38 / hg38:chr5 177169394; NSD1 GRCh38 / hg38:chr5 177200761; NSD1 GRCh38 / hg38:chr5 177247924; NSD1 GRCh38 / hg38:chr5 177275947; OPA1 GRCh38 / hg38:chr3 193628509; OPA1 GRCh38 / hg38:chr3 193603500; PCCA GRCh38 / hg38:chr13 100305751;PKP2GRCh38 / hg38:chr12 32894778;PPARAGRCh38 / hg38:chr22 46203575;PRPF3GRCh38 / hg38:chr1 150327557;PRPF3GRCh38 / hg38:chr1 150330401;SCN2AGRCh38 / hg38:chr2 165327155;SCN8AGRCh38 / hg38:chr12 51688758;SCN8AGRCh38 / hg38:chr12 51780202;SCN9AGRCh38 / hg38:chr2 166304329; SEMA3C GRCh38 / hg38:chr7 80794957; SEMA3D GRCh38 / hg38:chr7 85059541; SIRT3 GRCh38 / hg38:chr11 226081; STK11 GRCh38 / hg38:chr19 1216268; STK11 GRCh38 / hg38:chr19 1221621; SYNGAP1 GRCh38 / hg38:chr6 33448789; TOPORS GRCh38 / hg38:chr9 32551469; or VCAN GRCh38 / hg38:chr5 The target sequence is a sequence up to about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides, about 600 nucleotides, about 500 nucleotides, about 400 nucleotides, about 300 nucleotides, about 200 nucleotides, about 100 nucleotides, about 80 nucleotides, about 70 nucleotides, about 60 nucleotides, or about 50 nucleotides upstream (or 5'-side) of 83544965.

[0050]

[0133] In some embodiments, the ASO is selected from the group consisting of ABCB4 exon 8x, ASS1 exon 9x, ATP8B1 exon 16x, BAG3 exon 1x, CACNA1A exon 31x, CACNA1A exon 36x, CACNA1A exon 37x, CBS exon 3x, CBS exon 12x, CD55 exon 1x, CDKL5 exon 16x, CFH exon 3x, CHD2 exon 30x, CHRNA7 exon 4x, CISD2 exon 1x, CLN3 exon 15x, COL4A3 exon 11x, COL4A3 exon 41x, COL4A4 exon 22x, C OL4A4 exon 44x, DEPDC5 exon 20x, DHDDS exon 2x, ELOVL4 exon 3x, FAH exon 5x, FXN exon 4x, GALE exon 4x, GBE1 exon 3x, GRIN2A exon 11x, GRN exon 1x, HEXA exon 2x, KANSL1 exon 2x, KCNQ2 exon 1x, KMT2D exon 50x, MAPK3 exon 8x, MBD5 exon 13x, MECP2 exon 2x, MUT exon 11x , NF1 exon 31x, NIPBL exon 7x, NIPBL exon 38x, NSD1 exon 11x, OPA1 exon 6x, OPA1 exon 28x, OPTN exon 1x, PCCA exon 1x, PCCB exon 5x, PCCB exon 6x, PKP2 exon 4x, PLCB1 exon 23x, PRPF3 exon 3x, PRPF31 exon 9x, RAI1 exon 1x, RBFOX2 exon 5x, SCN2A exon 13x, SCN3A exon 6x , SCN3A exon 7x, SCN8A exon 4x, SCN8A exon 6x, SCN8A exon 20x, SCN9A exon 6x, SHANK3 exon 24x, SLC25A13 exon 3x, SLC25A13 exon 6x, SLC25A13 exon 9x, SLC25A13 exon 11x, SLC25A13 exon 13x, SLC6A1 exon 1x, SPTAN1 exon 12x, TEK exon 10x, TEK exon 15x, TOPORS exon 1x, The target sequence is approximately 1500 nucleotides, approximately 1000 nucleotides, approximately 800 nucleotides, approximately 700 nucleotides, approximately 600 nucleotides, approximately 500 nucleotides, approximately 400 nucleotides, approximately 300 nucleotides, approximately 200 nucleotides, approximately 100 nucleotides, approximately 80 nucleotides, approximately 70 nucleotides, approximately 60 nucleotides, or approximately 50 nucleotides downstream (or 3' side) of the 3' end of TSC2 exon 11x, TSC2 exon 30x, UBE3A exon 1x, or VCAN exon 7x.In some embodiments, the ASO is selected from the group consisting of AKT3GRCh38 / hg38:chr1 243564285; CACNA1AGRCh38 / hg38:chr19 13236449; CBSGRCh38 / hg38:chr21 43059730; CD46GRCh38 / hg38:chr1 207775745; CFHGRCh38 / hg38:chr1 196675529; CHD2GRCh38 / hg38:chr15 92998261; CLN3GRCh38 / hg38:chr16 28479644; COL11A2GRCh38 / hg38:chr6 33183634; COL4A3 GRCh38 / hg38:chr2 227296526; COL4A4 GRCh38 / hg38:chr2 227144653; COL4A4 GRCh38 / hg38:chr2 227015283; CR1 GRCh38 / hg38:chr1 207637848; CRX GRCh38 / hg38:chr19 47835579; CYP2J2 GRCh38 / hg38:chr1 59904366; DHDDS GRCh38 / hg38:chr1 26442372; DNAJC8 GRCh38 / hg38:chr1 28230131;EIF2AK3GRCh38 / hg38:chr2 88582755;ERN1GRCh38 / hg38:chr17 64102673;GALEGRCh38 / hg38:chr1 23798311;GUCY2FGRCh38 / hg38:chrX 109383365;GUCY2FGRCh38 / hg38:chrX 109439038;HEXAGRCh38 / hg38:chr15 72362376;HEXAGRCh38 / hg38:chr15 72345677;MAPK3GRCh38 / hg38:chr16 30115595;MBD5's GRCh38 / hg38:chr2 148460304;MBD5's GRCh38 / hg38:chr2 148490787;MBD5's GRCh38 / hg38:chr2 148505830;MUT's GRCh38 / hg38:chr6. 49436522; GRCh38 / hg38 in MYH14:chr19 50230999; GRCh38 / hg38 in MYO6:chr6 75867523; GRCh38 / hg38 in NF1:chr17 31250125; GRCh38 / hg38 in NF2:chr22 29628773; GRCh38 / hg38 in NIPBL:chr5 3 7048354;NR1H4 GRCh38 / hg38:chr12 100500024;NSD1 GRCh38 / hg38:chr5 177169559;NSD1 GRCh38 / hg38:chr5 177200783;NSD1 GRCh38 / hg38:chr5 177248079;NSD1 GRCh38 / hg38:chr5 177276101;OPA1 GRCh38 / hg38:chr3 193628616;OPA1 GRCh38 / hg38:chr3 193603557;PCCA GRCh38 / hg38:chr13 100305834; PKP2 GRCh38 / hg38:chr12 32894516; PPARA GRCh38 / hg38:chr22 46203752; PRPF3 GRCh38 / hg38:chr1 150327652; PRPF3 GRCh38 / hg38:chr1 150330498; SCN2A GRCh38 / hg38:chr2 165327202; SCN8A GRCh38 / hg38:chr12 51688849; SCN8A GRCh38 / hg38:chr12 51780271; SCN9A GRCh38 / hg38:chr2 166304238; SEMA3C GRCh38 / hg38:chr7 80794854; SEMA3D GRCh38 / hg38:chr7 85059498; SIRT3 GRCh38 / hg38:chr11 225673; STK11 GRCh38 / hg38:chr19 1216398; STK11 GRCh38 / hg38:chr19 1221846; SYNGAP1 GRCh38 / hg38:chr6 33448868; TOPORS GRCh38 / hg38:chr9 32551365; or VCAN GRCh38 / hg38:chr5 The target sequence is a sequence about 1500 nucleotides, about 1000 nucleotides, about 800 nucleotides, about 700 nucleotides, about 600 nucleotides, about 500 nucleotides, about 400 nucleotides, about 300 nucleotides, about 200 nucleotides, about 100 nucleotides, about 80 nucleotides, about 70 nucleotides, about 60 nucleotides, or about 50 nucleotides downstream (or 3') of 83545070.

[0051]

[0134] In some embodiments, the ASO is selected from the group consisting of ABCB4 exon 8x, ASS1 exon 9x, ATP8B1 exon 16x, BAG3 exon 1x, CACNA1A exon 31x, CACNA1A exon 36x, CACNA1A exon 37x, CBS exon 3x, CBS exon 12x, CD55 exon 1x, CDKL5 exon 16x, CFH exon 3x, CHD2 exon 30x, CHRNA7 exon 4x, CISD2 exon 1x, CLN3 exon 15x, COL4A ... exon 11x, COL4A3 exon 41x, COL4A4 exon 22x, COL4A4 exon 44x, DEPDC5 exon 20x, DHDDS exon 2x, ELOVL4 exon 3x, FAH exon 5x, FXN exon 4x, GALE exon 4x, GBE1 exon 3x, GRIN2A exon 11x, GRN exon 1x, HEXA exon 2x, KANSL1 exon 2x, KCNQ2 exon 1x, KMT2D exon 50x, MAPK3 exon 8x, MBD5 exon exon 13x, MECP2 exon 2x, MUT exon 11x, NF1 exon 31x, NIPBL exon 7x, NIPBL exon 38x, NSD1 exon 11x, OPA1 exon 6x, OPA1 exon 28x, OPTN exon 1x, PCCA exon 1x, PCCB exon 5x, PCCB exon 6x, PKP2 exon 4x, PLCB1 exon 23x, PRPF3 exon 3x, PRPF31 exon 9x, RAI1 exon 1x, RBFOX2 exon 5x, SCN2A exon 13x of SCN3A, exon 6x of SCN3A, exon 7x of SCN8A, exon 4x of SCN8A, exon 6x of SCN8A, exon 20x of SCN9A, exon 6x of SHANK3, exon 24x of SLC25A13, exon 3x of SLC25A13, exon 6x of SLC25A13, exon 9x of SLC25A13, exon 11x of SLC25A13, exon 13x of SLC6A1, exon 12x of SPTAN1, exon 10x of TEK, exon 15x of TEK, T The ASO targets sequences up to about 1500, 1000, 800, 700, 600, 500, 400, 300, 200, 100, 80, 70, 60, or 50 nucleotides downstream (or 3') of the 3' end of exon 1x of OPORS, exon 11x of TSC2, exon 30x of TSC2, exon 1x of UBE3A, or exon 7x of VCAN. In some embodiments, the ASO targets sequences up to about 1500, 1000, 800, 700, 600, 500, 400, 300, 200, 100, 80, 70, 60, or 50 nucleotides downstream (or 3') of AKT3 GRCh38 / hg38:chr1 243564285; CACNA1A GRCh38 / hg38:chr19 13236449; CBS GRCh38 / hg38:chr21 43059730; CD46 GRCh38 / hg38:chr1 207775745; CFH GRCh38 / hg38:chr1 196675529; CHD2 GRCh38 / hg38:chr15 92998261; CLN3 GRCh38 / hg38:chr16 28479644; COL11A2 GRCh38 / hg38:chr6 33183634; COL4A3 GRCh38 / hg38:chr2 227296526; COL4A4 GRCh38 / hg38:chr2 227144653; COL4A4 GRCh38 / hg38:chr2 227015283; CR1 GRCh38 / hg38:chr1 207637848; CRX GRCh38 / hg38:chr19 47835579; CYP2J2 GRCh38 / hg38:chr1 59904366; DHDDS GRCh38 / hg38:chr1 26442372; DNAJC8 GRCh38 / hg38:chr1 28230131; EIF2AK3 GRCh38 / hg38:chr2 88582755; ERN1 GRCh38 / hg38:chr17 64102673;GALEGRCh38 / hg38:chr1 23798311;GUCY2FGRCh38 / hg38:chrX 109383365;GUCY2FGRCh38 / hg38:chrX 109439038;HEXAGRCh38 / hg38:chr15 72362376;HEXAGRCh38 / hg38:chr15 72345677;MAPK3GRCh38 / hg38:chr16 30115595;MBD5GRCh38 / hg38:chr2 148460304;MBD5GRCh38 / hg38:chr2 148490787; MBD5 GRCh38 / hg38:chr2 148505830; MUT GRCh38 / hg38:chr6 49436522; MYH14 GRCh38 / hg38:chr19 50230999; MYO6 GRCh38 / hg38:chr6 75867523; NF1 GRCh38 / hg38:chr17 31250125; NF2 GRCh38 / hg38:chr22 29628773; NIPBL GRCh38 / hg38:chr5 37048354; NR1H4 GRCh38 / hg38:chr12 100500024; NSD1 GRCh38 / hg38:chr5 177169559; NSD1 GRCh38 / hg38:chr5 177200783; NSD1 GRCh38 / hg38:chr5 177248079; NSD1 GRCh38 / hg38:chr5 177276101; OPA1 GRCh38 / hg38:chr3 193628616; OPA1 GRCh38 / hg38:chr3 193603557; PCCA GRCh38 / hg38:chr13 100305834; PKP2 GRCh38 / hg38:chr12 32894516; PPARA GRCh38 / hg38:chr22 46203752; PRPF3 GRCh38 / hg38:chr1 150327652; PRPF3 GRCh38 / hg38:chr1 150330498; SCN2A GRCh38 / hg38:chr2 165327202; SCN8A GRCh38 / hg38:chr12 51688849; SCN8A GRCh38 / hg38:chr12 51780271; SCN9A GRCh38 / hg38:chr2 166304238; SEMA3C GRCh38 / hg38:chr7 80794854; SEMA3D GRCh38 / hg38:chr7 85059498; SIRT3 GRCh38 / hg38:chr11 225673; STK11 GRCh38 / hg38:chr19 1216398; STK11 GRCh38 / hg38:c The target sequences are located up to about 1500, 1000, 800, 700, 600, 500, 400, 300, 200, 100, 80, 70, 60, or 50 nucleotides downstream (or 3') of hr19 1221846; GRCh38 / hg38:chr6 33448868 of SYNGAP1; GRCh38 / hg38:chr9 32551365 of TOPORS; or GRCh38 / hg38:chr5 83545070 of VCAN.

[0052]

[0135] In some embodiments, the ASO has a sequence complementary to a targeted portion of an NMD exon mRNA of any one of SEQ ID NOs: 60-191.

[0136] In some embodiments, the ASO targets a sequence upstream from the 5' end of an NIE, for example, an NIE (e.g., exon 8x of ABCB4, exon 9x of ASS1, exon 16x of ATP8B1, exon 1x of BAG3, exon 31x of CACNA1A, exon 36x of CACNA1A, exon 37x of CACNA1A, exon 3x of CBS, exon 12x of CBS, exon 1x of CD55, exon 16x of CDKL5, exon 3x of CFH, exon 30x of CHD2, exon 4x of CHRNA7, exon 1x of CISD2, exon 15x of CLN3, exon 1 of COL4A3). 1x, COL4A3 exon 41x, COL4A4 exon 22x, COL4A4 exon 44x, DEPDC5 exon 20x, DHDDS exon 2x, ELOVL4 exon 3x, FAH exon 5x, FXN exon 4x, GALE exon 4x, GBE1 exon 3x, GRIN2A exon 11x, GRN exon 1x, HEXA exon 2x, KANSL1 exon 2x, KCNQ2 exon 1x, KMT2D exon 50x, MAPK3 exon 8x, MBD5 exon 1 3x, MECP2 exon 2x, MUT exon 11x, NF1 exon 31x, NIPBL exon 7x, NIPBL exon 38x, NSD1 exon 11x, OPA1 exon 6x, OPA1 exon 28x, OPTN exon 1x, PCCA exon 1x, PCCB exon 5x, PCCB exon 6x, PKP2 exon 4x, PLCB1 exon 23x, PRPF3 exon 3x, PRPF31 exon 9x, RAI1 exon 1x, RBFOX2 exon 5x, SCN2A exon 13x of SCN3A, exon 6x of SCN3A, exon 7x of SCN8A, exon 4x of SCN8A, exon 6x of SCN8A, exon 20x of SCN9A, exon 6x of SHANK3, exon 24x of SLC25A13, exon 3x of SLC25A13, exon 6x of SLC25A13, exon 9x of SLC25A13, exon 11x of SLC25A13, exon 13x of SLC6A1, exon 12x of SPTAN1, exon 10x of TEK, exon 15x of TEK,ASOs targeting sequences upstream from the 5' end of TOPORS exon 1x, TSC2 exon 11x, TSC2 exon 30x, UBE3A exon 1x, or VCAN exon 7x comprise sequences that are at least about 80%, 85%, 90%, 95%, 97%, or 100% complimentary to at least eight consecutive nucleic acids of any one of SEQ ID NOs: 60-134. For example, NIE (e.g., exons of AKT3 (GRCh38 / hg38:chr1 243564285 243564388); exons of CACNA1A (GRCh38 / hg38:chr19 13236449 13236618); exons of CBS (GRCh38 / hg38:chr21 43059730 43060012); exons of CD46 (GRCh38 / hg38:chr1 207775610 207775745); exons of CFH (GRCh38 / hg38:chr1 196675450 196675529); exons of CHD2 (GRCh38 / hg38:chr15 92998149 92998261); exons of CLN3 (GRCh38 / hg38:chr16 28479644 28479765); exons of COL11A2 (GRCh38 / hg38:chr6 33183, 634 33183698); COL4A3 exon (GRCh38 / hg38:chr2 227296487 227296526); COL4A4 exon (GRCh38 / hg38:chr2 227144653 227144833); COL4A4 exon (GRCh38 / hg38:chr2 227015283 227015360); CR1 exon (GRCh38 / hg38:chr1 207637688 207637848); CRX exon (GRCh38 / hg38:chr19 47835403 47835579); CYP2J2 exon (GRCh38 / hg38:chr1 59904366 59904516; DHDDS exons (GRCh38 / hg38:chr1 26442335 26442372); DNAJC8 exons (GRCh38 / hg38:chr1 28230131 28230252); EIF2AK3 exons (GRCh38 / hg38:chr2 88582755 88582824); ERN1 exons (GRCh38 / hg38:chr17 64102673 64102804); GALE exons (GRCh38 / hg38:chr1 23798311 23798484); GUCY2F exons (GRCh38 / hg38:chrX 109383365 109383446); GUCY2F exon (GRCh38 / hg38:chrX 109439038 109439175); HEXA exon (GRCh38 / hg38:chr15 72362376 72362466); HEXA exon (GRCh38 / hg38:chr15 72345677 72345776); MAPK3 exon (GRCh38 / hg38:chr16 30115595 30115645); MBD5 exon (GRCh38 / hg38:chr2 148460219 148460304); MBD5 exon (GRCh38 / hg38:chr2 148490695 148490787);MBD5 exon (GRCh38 / hg38:chr2 148505761 148505830);MUT exon (GRCh38 / hg38:chr6 49436522 49436597);Exons of MYH14 (GRCh38 / hg38:chr19 50230825 50230999); exons of MYO6 (GRCh38 / hg38:chr6 75867431 75867523); exons of NF1 (GRCh38 / hg38:chr17 31249955 31250125); exons of NF2 (GRCh38 / hg38:chr22 29628658 29628773); exons of NIPBL (GRCh38 / hg38:chr5 37048127 37048354); exons of NR1H4 (GRCh38 / hg38:chr12 100499841) 100500024); NSD1 exon (GRCh38 / hg38:chr5 177169394 177169559); NSD1 exon (GRCh38 / hg38:chr5 177200761 177200783); NSD1 exon (GRCh38 / hg38:chr5 177247924 177248079); NSD1 exon (GRCh38 / hg38:chr5 177275947 177276101); OPA1 exon (GRCh38 / hg38:chr3 193628509 193628616); OPA1 exon (GRCh38 / hg38:chr3 193603500 193603557); PCCA exon (GRCh38 / hg38:chr13 100305751 100305834); PKP2 exon (GRCh38 / hg38:chr12 32894516 32894778); PPARA exon (GRCh38 / hg38:chr22 46203575 46203752); PRPF3 exon (GRCh38 / hg38:chr1 150327557 150327652); PRPF3 exon (GRCh38 / hg38:chr1 150330401 150330498); SCN2A exon (GRCh38 / hg38:chr2 165327155 165327202); exons of SCN8A (GRCh38 / hg38:chr12 51688758 51688849); exons of SCN8A (GRCh38 / hg38:chr12 51780202; 51780271); exon of SCN9A (GRCh38 / hg38:chr2 166304238 166304329); exon of SEMA3C (GRCh38 / h exons of SEMA3D (GRCh38 / hg38:chr7 80794854 80794957); exons of SIRT3 (GRCh38 / hg38:chr11 225673 226081); exons of STK11 (GRCh38 / hg38:chr19 1216268 1216398); exons of STK11 (GRCh38 / hg38:chr19 1221621 1221846); exons of SYNGAP1 (GRCh38 / hg38:chr6 33448789 33448868); exons of TOPORS (GRCh38 / hg38:chr9 32551365 32551469); ASOs targeting sequences upstream from the 5' end of an exon of VCAN (GRCh38 / hg38:chr5 83544965 83545070) can include sequences having at least 80%, 85%, 90%, 95%, 97%, or 100% sequence identity to any one of SEQ ID NOs: 135-191.

[0053]

[0137] In some embodiments, the ASO targets a sequence containing an exon-intron boundary (or junction). For example, an ASO targeting a sequence containing an exon-intron boundary can include a sequence that is at least about 80%, 85%, 90%, 95%, 97%, or 100% complementary to at least eight contiguous nucleic acids of any one of SEQ ID NOs: 60-191. In some embodiments, the ASO targets a sequence downstream from the 3' end of the NIE. For example, NIE (e.g., exon 8x of ABCB4, exon 9x of ASS1, exon 16x of ATP8B1, exon 1x of BAG3, exon 31x of CACNA1A, exon 36x of CACNA1A, exon 37x of CACNA1A, exon 3x of CBS, exon 12x of CBS, exon 1x of CD55, exon 16x of CDKL5, exon 3x of CFH, exon 30x of CHD2, exon 31x of CACNA1A, exon 37x of CACNA1A, exon 3x of CBS, exon 12x of CBS, exon 1x of CD55, exon 16x of CDKL5, exon 3x of CFH, exon 30x of CHD2, exon 30x of CHRNA7) 4x, CISD2 exon 1x, CLN3 exon 15x, COL4A3 exon 11x, COL4A3 exon 41x, COL4A4 exon 22x, COL4A4 exon 44x, DEPDC5 exon 20x, DHDDS exon 2x, ELOVL4 exon 3x, FAH exon 5x, FXN exon 4x, GALE exon 4x, GBE1 exon 3x, GRIN2A exon 11x, GRN exon exon 1x, HEXA exon 2x, KANSL1 exon 2x, KCNQ2 exon 1x, KMT2D exon 50x, MAPK3 exon 8x, MBD5 exon 13x, MECP2 exon 2x, MUT exon 11x, NF1 exon 31x, NIPBL exon 7x, NIPBL exon 38x, NSD1 exon 11x, OPA1 exon 6x, OPA1 exon 28x, OPTN exon 1 x, PCCA exon 1x, PCCB exon 5x, PCCB exon 6x, PKP2 exon 4x, PLCB1 exon 23x, PRPF3 exon 3x, PRPF31 exon 9x, RAI1 exon 1x, RBFOX2 exon 5x, SCN2A exon 13x, SCN3A exon 6x, SCN3A exon 7x, SCN8A exon 4x, SCN8A exon 6x, SCN8A exon 20x,ASOs targeting sequences downstream from the 3' end of SCN9A exon 6x, SHANK3 exon 24x, SLC25A13 exon 3x, SLC25A13 exon 6x, SLC25A13 exon 9x, SLC25A13 exon 11x, SLC25A13 exon 13x, SLC6A1 exon 1x, SPTAN1 exon 12x, TEK exon 10x, TEK exon 15x, TOPORS exon 1x, TSC2 exon 11x, TSC2 exon 30x, UBE3A exon 1x, or VCAN exon 7x can include sequences having at least 80%, 85%, 90%, 95%, 97%, or 100% sequence identity to any one of SEQ ID NOs: 60-134. For example, NIE (e.g., exons of AKT3 (GRCh38 / hg38:chr1 243564285 243564388); exons of CACNA1A (GRCh38 / hg38:chr19 13236449 13236618); exons of CBS (GRCh38 / hg38:chr21 43059730 430, 60012); CD46 exon (GRCh38 / hg38:chr1 207775610 207775745); CFH exon (GRCh38 / hg38:chr1 exons of CHD2 (GRCh38 / hg38:chr15 92998149 92998261); exons of CLN3 (GRCh38 / hg38:chr16 28479644 28479765); exons of COL11A2 (GRCh38 / hg38:chr6 33183634 33183698); exons of COL4A3 (GRCh38 / hg38:chr2 227296487 227296526); exons of COL4A4 (GRCh38 / hg38:chr2 227144653) 227144833; exons of COL4A4 (GRCh38 / hg38:chr2 227015283 227015360); exons of CR1 (GRCh38 / hg38:chr1 207637688 207637848); exons of CRX (GRCh38 / hg38:chr19 47835403 47835579); exons of CYP2J2 (GRCh38 / hg38:chr1 59904366 59904516); exons of DHDDS (GRCh38 / hg38:chr1 26442335 26442372); exons of DNAJC8 (GRCh38 / hg38:chr1 28230131) 28230252); EIF2AK3 exon (GRCh38 / hg38:chr2 88582755 88582824); ERN1 exon (GRCh38 / hg38:chr17 64102673 64102804); GALE exon (GRCh38 / hg38:chr1 23798311 23798484); GUCY2F exon (GRCh38 / hg38:chrX 109383365 109383446); GUCY2F exon (GRCh38 / hg38:chrX 109439038 109439175); HEXA exon (GRCh38 / hg38:chr15 72362376 72362466); HEXA exon (GRCh38 / hg38:chr15 72345677 72345776); MAPK3 exon (GRCh38 / hg38:chr16 30115595 30115645); MBD5 exon (GRCh38 / hg38:chr2 148460219 148460304);MBD5 exon (GRCh38 / hg38:chr2 148490695 148490787); MBD5 exon (GRCh38 / hg38:chr2 148505761 148505830); MUT exon (GRCh38 / hg38:chr6 49436522 49436597); MYH14 exon (GRCh38 / hg38:chr19 50230825 50230999); MYO6 exon (GRCh38 / hg38:chr6 75867431 75867523); NF1 exon (GRCh38 / hg38:chr17 31249955 31250125); exons of NF2 (GRCh38 / hg38:chr22 29628658 29628773); exons of NIPBL (GRCh38 / hg38:chr5 37048127 37048354); exons of NR1H4 (GRCh38 / hg38:chr12 100499841 100500024); exons of NSD1 (GRCh38 / hg38:chr5 177169394 177169559); exons of NSD1 (GRCh38 / hg38:chr5 177200761 177200783); exons of NSD1 (GRCh38 / hg38:chr5 177247924 177248079; NSD1 exon (GRCh38 / hg38:chr5 177275947 177276101); OPA1 exon (GRCh38 / hg38:chr3 193628509 193628616); OPA1 exon (GRCh38 / hg38:chr3 193603500 193603557); PCCA exon (GRCh38 / hg38:chr13 100305751 100305834); PKP2 exon (GRCh38 / hg38:chr12 32894516 32894778); PPARA exon (GRCh38 / hg38:chr22 46203575 46203752); exon of PRPF3 (GRCh38 / hg38:chr1 150327557 150327652); exon of PRPF3 (GRCh38 / hg38:chr1 1503; 30401 150330498; SCN2A exon (GRCh38 / hg38:chr2 165327155 165327202); SCN8A exon (GRCh38 / hg38:chr12 51688758 51688849); SCN8A exon (GRCh38 / hg38:chr12 51780202 51780271); SCN9A exon (GRCh38 / hg38:chr2 166304238 166304329); SEMA3C exon (GRCh38 / hg38:chr7 80794854 80794957); SEMA3D exon (GRCh38 / hg38:chr7 85059498 85059541; SIRT3 exons (GRCh38 / hg38:chr11 225673 226081); STK11 exons (GRCh38 / hg38:chr19 1216268 1216398); STK11 exons (GRCh38 / hg38:chr19 1221621 1221846); SYNGAP1 exons (GRCh38 / hg38:chr6 33448789 33448868); TOPORS exons (GRCh38 / hg38:chr9 ASOs targeting sequences downstream from the 3' end of exons (GRCh38 / hg38:chr5 83544965 83545070) of VCAN can include sequences having at least 80%, 85%, 90%, 95%, 97%, or 100% sequence identity to any one of SEQ ID NOs: 135-191. In some embodiments, the ASO targets a sequence within an NIE.

[0054]

[0138] In some embodiments, the ASO comprises exon 8x of ABCB4 NIE-containing pre-mRNA comprising NIE exon 8, exon 9x of ASS1 NIE-containing pre-mRNA comprising NIE exon 9, exon 16x of ATP8B1 NIE-containing pre-mRNA comprising NIE exon 16, exon 1x of BAG3 NIE-containing pre-mRNA comprising NIE exon 1, exon 31x of CACNA1A NIE-containing pre-mRNA comprising NIE exon 31, exon 36x of CACNA1A NIE-containing pre-mRNA comprising NIE exon 36, exon 37x of CACNA1A NIE-containing pre-mRNA comprising NIE exon 37, exon 3x of CBS NIE-containing pre-mRNA comprising NIE exon 3, exon 12x of CBS NIE-containing pre-mRNA comprising NIE exon 12, exon 1x of CD55 NIE-containing pre-mRNA comprising NIE exon 1, and CDKL5 CFH, containing exon 16x of NIE-containing pre-mRNA and NIE exon 3 CHD2, containing exon 3x of NIE-containing pre-mRNA and NIE exon 30 CHRNA7, containing exon 4x of NIE-containing pre-mRNA and NIE exon 1 CISD2, containing exon 1x of NIE-containing pre-mRNA and NIE exon 15 CLN3, containing exon 15x of NIE-containing pre-mRNA and NIE exon 11 COL4A3, containing exon 11x of NIE-containing pre-mRNA and NIE exon 41 COL4A3, containing exon 41x of NIE-containing pre-mRNA and NIE exon 22 COL4A4, containing exon 22x of NIE-containing pre-mRNA and NIE exon 44 DEPDC5, containing exon 44x of NIE-containing pre-mRNA and NIE exon 20 DHDDS, which contains exon 20x of NIE-containing pre-mRNA and NIE exon 2; ELOVL4, which contains exon 2x of NIE-containing pre-mRNA and NIE exon 3 exon 3x of NIE-containing pre-mRNA, exon 5x of FAH NIE-containing pre-mRNA containing NIE exon 5, exon 4x of FXN NIE-containing pre-mRNA containing NIE exon 4, exon 4x of GALE NIE-containing pre-mRNA containing NIE exon 4, exon 3x of GBE1 NIE-containing pre-mRNA containing NIE exon 3, exon 11x of GRIN2A NIE-containing pre-mRNA containing NIE exon 11, exon 1x of GRN NIE-containing pre-mRNA containing NIE exon 1, exon 2x of HEXA NIE-containing pre-mRNA containing NIE exon 2, exon 2x of KANSL1 NIE-containing pre-mRNA containing NIE exon 2, exon 2x of KCNQ2 NIE-containing pre-mRNA containing NIE exon 1, exon 1x of NIE-containing pre-mRNA containing NIE exon 50 KMT2D NIE-containing pre-mRNA exon 50x, MAPK3 NIE-containing pre-mRNA exon 8, MBD5 NIE-containing pre-mRNA exon 13x, MECP2 NIE-containing pre-mRNA exon 2x, MUT NIE-containing exon 11x, NF1 NIE-containing pre-mRNA exon 31x, NIPBL NIE-containing exon 7x, NIPBL NIE-containing pre-mRNA exon 38x, NSD1 NIE-containing exon 11x, OPA1 NIE-containing exon 6, OPA1 NIE-containing exon 6x, NIE-containing pre-mRNA exon 28 OPTN containing exon 28x of NIE-containing pre-mRNA and NIE exon 1 PCCA containing exon 1x of NIE-containing pre-mRNA and NIE exon 1 PCCB containing exon 5x of NIE-containing pre-mRNA and NIE exon 5 PCCB containing exon 6x of NIE-containing pre-mRNA and NIE exon 6 PKP2 containing exon 4x of NIE-containing pre-mRNA and NIE exon 23 PLCB1 containing exon 23x of NIE-containing pre-mRNA and NIE exon 3 PRPF3 containing exon 3x of NIE-containing pre-mRNA and NIE exon 9 PRPF31 containing exon 9x of NIE-containing pre-mRNA and NIE exon 1 RAI1 containing exon 1x of NIE-containing pre-mRNA and NIE exon 5 RBFOX2 containing exon 5x of NIE-containing pre-mRNA and NIE exon 13 SCN2A containing exon 5x of NIE-containing pre-mRNA and NIE exon 13 Exon 13x of NIE-containing pre-mRNA, SCN3A containing NIE exon 6, Exon 6x of NIE-containing pre-mRNA, SCN3A containing NIE exon 7, Exon 7x of NIE-containing pre-mRNA, SCN8A containing NIE exon 4, Exon 4x of NIE-containing pre-mRNA, SCN8A containing NIE exon 6, Exon 6x of NIE-containing pre-mRNA, SCN8A containing NIE exon 20exon 20x of NIE-containing pre-mRNA, SCN9A containing NIE exon 6, exon 6x of NIE-containing pre-mRNA, SHANK3 containing NIE exon 24, exon 24x of NIE-containing pre-mRNA, SLC25A13 containing NIE exon 3, exon 3x of NIE-containing pre-mRNA, SLC25A13 containing NIE exon 6, exon 6x of NIE-containing pre-mRNA, SLC25A13 containing NIE exon 9, exon 9x of NIE-containing pre-mRNA, SLC25A13 containing NIE exon 11, SLC25A13 containing NIE exon 13x of NIE-containing pre-mRNA, SLC6A1 containing NIE exon 1x of NIE-containing pre-mRNA, SPTAN1 containing NIE exon 12, TEK containing NIE exon 10 Target exon 10x of NIE-containing pre-mRNA, exon 15x of TEK NIE-containing pre-mRNA containing NIE exon 15, exon 1x of TOPORS NIE-containing pre-mRNA containing NIE exon 1, exon 11x of TSC2 NIE-containing pre-mRNA containing NIE exon 11, exon 30x of TSC2 NIE-containing pre-mRNA containing NIE exon 30, exon 1x of UBE3A NIE-containing pre-mRNA containing NIE exon 1, or exon 7x of VCAN NIE-containing pre-mRNA containing NIE exon 7. In some embodiments, the ASO is selected from the group consisting of exon 8x of ABCB4 pre-mRNA, exon 9x of ASS1 pre-mRNA, exon 16x of ATP8B1 pre-mRNA, exon 1x of BAG3 pre-mRNA, exon 31x of CACNA1A pre-mRNA, exon 36x of CACNA1A pre-mRNA, exon 37x of CACNA1A pre-mRNA, exon 3x of CBS pre-mRNA, exon 12x of CBS pre-mRNA, exon 1x of CD55 pre-mRNA, exon 16x of CDKL5 pre-mRNA, exon 3x of CFH pre-mRNA, exon 30x of CHD2 pre-mRNA, exon 4x of CHRNA7 pre-mRNA, exon 1x of CISD2 pre-mRNA, and CLN3Pre-mRNA exon 15x, COL4A3 pre-mRNA exon exon 11x, COL4A3 pre-mRNA exon 41x, COL4A4 pre-mRNA exon 22x, COL4A4 pre-mRNA exon 44x, DEPDC5 pre-mRNA exon 20x, DHDDS pre-mRNA exon 2x, ELOVL4 pre-mRNA exon 3x, FAH pre-mRNA exon 5x, FXN pre-mRNA exon 4x, GALE pre-mRNA exon 4x, GBE1 pre-mRNA exon 3x, GRIN2A pre-mRNA exon 1x, GRN pre-mRNA exon 1x, HEXA pre-mRNA exon 2x, KANSL1 pre-mRNA exon 2x, KCNQ2 pre-mRNA exon 1x, KMT2D pre-mRNA exon 50x, MAPK3 pre-mRNA exon 8x, MBD5 pre-mRNA exon 13x, MECP2 pre-mRNA exon 2x, MUT pre-mRNA exon 11x, NF1 Pre-mRNA exon 31x, NIPBL pre-mRNA exon 7x, NIPBL pre-mRNA exon 38x, NSD1 pre-mRNA exon 11x, OPA1 pre-mRNA exon 6x, OPA1 pre-mRNA exon 28x, OPTN pre-mRNA exon 1x, PCCA pre-mRNA exon 1x, PCCB pre-mRNA exon 5x, PCCB pre-mRNA exon 6x, PKP2 pre-mRNA exon 4x, PLCB1 pre-mRNA exon 23x, PRPF3 pre-mRNA exon 3x, PRPF31 pre-mRNA exon 9x, RAI1 pre-mRNA exon 1x, RBFOX2 pre-mRNA exon 5x, SCN2A pre-mRNA exon 13x, SCN3A pre-mRNA exon 6x, SCN3A pre-mRNA exon 7x, SCN8A pre-mRNA exon 4x, SCN8A pre-mRNA exon 6x, SCN8A Pre-mRNA exon 20x, SCN9A pre-mRNA exon 6x, SHANK3 pre-mRNA exon 24x, SLC25A13 pre-mRNA exon 3x, SLC25A13 pre-mRNA exon 6x, SLC25A13The target sequences are located downstream (or 3') of the 5' end of exon 9x of pre-mRNA, exon 11x of SLC25A13 pre-mRNA, exon 13x of SLC25A13 pre-mRNA, exon 1x of SLC6A1 pre-mRNA, exon 12x of SPTAN1 pre-mRNA, exon 10x of TEK pre-mRNA, exon 15x of TEK pre-mRNA, exon 1x of TOPORS pre-mRNA, exon 11x of TSC2 pre-mRNA, exon 30x of TSC2 pre-mRNA, exon 1x of UBE3A pre-mRNA, or exon 7x of VCAN pre-mRNA. In some embodiments, the ASO is selected from the group consisting of exon 8x of ABCB4 pre-mRNA, exon 9x of ASS1 pre-mRNA, exon 16x of ATP8B1 pre-mRNA, exon 1x of BAG3 pre-mRNA, exon 31x of CACNA1A pre-mRNA, exon 36x of CACNA1A pre-mRNA, exon 37x of CACNA1A pre-mRNA, exon 3x of CBS pre-mRNA, exon 12x of CBS pre-mRNA, exon 1x of CD55 pre-mRNA, exon 16x of CDKL5 pre-mRNA, exon 3x of CFH pre-mRNA, exon 30x of CHD2 pre-mRNA, exon 4x of CHRNA7 pre-mRNA, exon 1x of CISD2 pre-mRNA, exon 15x of CLN3 pre-mRNA, exon 11x of COL4A3 pre-mRNA, exon 41x of COL4A3 pre-mRNA, exon 22x of COL4A4 pre-mRNA, and exon 1x of COL4A4 pre-mRNA. Pre-mRNA exon 44x, DEPDC5 pre-mRNA exon 20x, DHDDS pre-mRNA exon 2x, ELOVL4 pre-mRNA exon 3x, FAH pre-mRNA exon 5x, FXN pre-mRNA exon 4x, GALE pre-mRNA exon 4x, GBE1 pre-mRNA exon 3x, GRIN2A pre-mRNA exon 11x of the GRN pre-mRNA, exon 1x of the HEXA pre-mRNA exon 2x of the body, exon 2x of the KANSL1 pre-mRNA, exon 1x of the KCNQ2 pre-mRNA, exon 50x of the KMT2D pre-mRNA, exon 8x of the MAPK3 pre-mRNA, exon 13x of the MBD5 pre-mRNA, exon 2x of the MECP2 pre-mRNA, exon 11x of the MUT pre-mRNA, NF1 Pre-mRNA exon 31x, NIPBL pre-mRNA exon 7x, NIPBL pre-mRNA exon 38x, NSD1 pre-mRNA exon 11x, OPA1 pre-mRNA exon 6x, OPA1 pre-mRNA exon 28x, OPTN pre-mRNA exon 1x, PCCA pre-mRNA exon 1x, PCCB pre-mRNA exon 5x, PCCB pre-mRNA exon 6x, PKP2 pre-mRNA exon 4x, PLCB1 pre-mRNA exon 23x, PRPF3 pre-mRNA exon 3x, PRPF31 pre-mRNA exon 9x, RAI1 pre-mRNA exon 1x, RBFOX2 pre-mRNA exon 5x, SCN2A pre-mRNA exon 13x, SCN3A pre-mRNA exon 6x, SCN3A pre-mRNA exon 7x, SCN8A pre-mRNA exon 4x, SCN8A pre-mRNA exon 6x, SCN8A Pre-mRNA exon 20x, SCN9A pre-mRNA exon 6x, SHANK3 pre-mRNA exon 24x, SLC25A13 pre-mRNA exon 3x, SLC25A13 pre-mRNA exon 6x, SLC25A13 pre-mRNA exon 9x, SLC25A13 pre-mRNA exon 11x, SLC25A13 pre-mRNA exon 13x, SLC6A1 pre-mRNA exon 1x, SPTAN1 pre-mRNA exon 12x, TEK pre-mRNA exon 10x, TEK pre-mRNA exon 15x, TOPORS pre-mRNA exon 1x, TSC2 pre-mRNA exon 11x, TSC2 pre-mRNA exon 30x, UBE3A pre-mRNA exon 1x, or VCAN It targets exon 20x sequences upstream (or 5') from the 3' end of exon 7x of the pre-mRNA.

[0055]

[0139] In some embodiments, the inhibitors of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, P LCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, C D46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 The targeted portion of the NIE-containing pre-mRNA is in intron 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50. In some embodiments, hybridization of the ASO to the targeting portion of the NIE pre-mRNA results in exon skipping of at least one NIE within intron 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50, followed by exon skipping of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, or 56. , CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL 1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SC Increases N2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein production. In some embodiments, the inhibitors of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, M APK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBF OX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, or VCAN The targeting moieties of NIE-containing pre-mRNAs are intron 8 of ABCB4, intron 9 of ASS1, intron 16 of ATP8B1, intron 1 of BAG3, intron 31 of CACNA1A, intron 36 of CACNA1A, intron 37 of CACNA1A, intron 3 of CBS, intron 12 of CBS, intron 1 of CD55, intron 16 of CDKL5, intron 3 of CFH, intron 30 of CHD2, intron 4 of CHRNA7, intron 1 of CISD2,CLN3 intron 15, COL4A3 intron 11, COL4A3 intron 41, COL4A4 intron 22, COL4A4 intron 44, DEPDC5 intron 20, DHDDS intron 2, ELOVL4 intron 3, FAH intron 5, FN intron 4, GALE intron 4, GBE1 intron 3, GRIN2A intron 11, GRN intron 1, HEA intron 2, K ANSL1 intron 2, KMT2D intron 50, MAPK3 intron 8, MBD5 intron 13, MECP2 intron 2, MUT intron 11, NF1 intron 31, NIPBL intron 7, NIPBL intron 38, NSD1 intron 11, OPA1 intron 6, OPA1 intron 28, OPTN intron 1, PCCA intron 1, PCCB intron 5, PCCB intron intron 6, intron 4 of PKP2, intron 23 of PLCB1, intron 3 of PRPF3, intron 9 of PRPF31, intron 1 of RAI1, intron 5 of RBFO2, intron 13 of SCN2A, intron 6 of SCN3A, intron 7 of SCN3A, intron 4 of SCN8A, intron 6 of SCN8A, intron 20 of SCN8A, intron 6 of SCN9A, intron 24 of SHANK3, SLC25A1 3 intron 3, SLC25A13 intron 6, SLC25A13 intron 9, SLC25A13 intron 11, SLC25A13 intron 13, SLC6A1 intron 1, SPTAN1 intron 12, TEK intron 10, TEK intron 15, TOPORS intron 1, TSC2 intron 11, TSC2 intron 30, UBE3A intron 1, or VCAN intron 7. In some embodiments, AKT3, CACNA1A, CBS, CD46, CFH, CHD2, CLN3, COL11A2, COL4A3, COL4A4, COL4A4, CR1, CRX, CYP2J2, DHDDS, DNAJC8, EIF2AK3, ERN1, GALE, GUCY2F, GUCY2F, HEXA, HEXA, MAPK3, MBD5, MBD5, MBD5, MBD5, MUT, MYH14, MYO6, NF1, NF2, NIPBL, NR1H4, NSD1,The targeting moieties of NSD1, NSD1, NSD1, OPA1, OPA1, PCCA, PKP2, PPARA, PRPF3, PRPF3, SCN2A, SCN8A, SCN8A, SCN9A, SEMA3C, SEMA3D, SIRT3, STK11, STK11, SYNGAP1, TOPORS, or VCAN NIE-containing pre-mRNAs are located in the intron of AKT3 (GRCh38 / hg38:chr1 243563849 243572925); intron of CACNA1A (GRCh38 / hg38:chr19 13235731 13241520); intron of CBS (GRCh38 / hg38:chr21 43059304 43060440); CD46 intron (GRCh38 / hg38:chr1 207770363 207783291); CFH intron (GRCh38 / hg38:chr1 196673963 196675988); CHD2 intron (GRCh38 / hg38:chr15 92997404 92998498); CLN3 intron (GRCh38 / hg38:chr16 28477878 28482104); COL11A2 intron (GRCh38 / hg38:chr6 33181172 33184144); COL4A3 intron (GRCh38 / hg38:chr2 227295317 227297673; COL4A4 intron (GRCh38 / hg38:chr2 227144559 227147412); COL4A4 intron (GRCh38 / hg38:chr2 227012299 227022047); CR1 intron (GRCh38 / hg38:chr1 207630622 207639396); CRX intron (GRCh38 / hg38:chr19 47834544 47836242); CYP2J2 intron (GRCh38 / hg38:chr1 59901104 59904870); DHDDS intron (GRCh38 / hg38:chr1 26438285 26442730); intron of DNAJC8 (GRCh38 / hg38:chr1 28229025 28232920); intron of EIF2AK3 (GRCh38 / hg38:chr2 88579641 88583429);intron of ERN1 (GRCh38 / hg38:chr17 64098242 64129975); intron of GALE (GRCh38 / hg38:chr1 23798231 23798614); intron of GUCY2F (GRCh38 / hg38:chrx 109382213; 109385183); GUCY2F intron (GRCh38 / hg38:chrx 109430397 109441350); HEXA intron (GRCh38 / hg38:chr15 72356651 72375719); HEXA intron (GRCh38 / hg38:chr15 72345552 72346234); MAPK3 intron (GRCh38 / hg38:chr16 30114709 30116635); MBD5 intron (GRCh38 / hg38:chr2 148458872 148462581); MBD5 intron (GRCh38 / hg38:chr2 148490595 148502435); intron of MBD5 (GRCh38 / hg38:chr2 148502510 148510059); intron of MUT (GRCh38 / hg38:chr6 49435625 49440205); intron of MYH14 (GRCh38 / hg38:chr19 50230624 50231929); intron of MYO6 (GRCh38 / hg38:chr6 75867106 75870646); intron of NF1 (GRCh38 / hg38:chr17 31249120 31252937); intron of NF2 (GRCh38 / hg38:chr22 29604113 29636750); intron of NIPBL (GRCh38 / hg38:chr5 37046200 37048501); intron of NR1H4 (GRCh38 / hg38:chr12 100493403 100505574); intron of NSD1 (GRCh38 / hg38:chr5 177136031 177191883); intron of NSD1 (GRCh38 / hg38:chr5 177192020 177204119); intron of NSD1 (GRCh38 / hg38:chr5 177246797 177248180); intron of NSD1 (GRCh38 / hg38:chr5 177273785 17728 0564); OPA1 intron (GRCh38 / hg38:chr3 193626203 193631611); OPA1 intron (GRCh38 / hg38:chr3 193593374 193614710); PCCA intron (GRCh38 / hg38:chr13 100302999 100307191); PKP2 intron (GRCh38 / hg38:chr12 32879033 32896508) PPARA intron (GRCh38 / hg38:chr22 46198592 46215172); PRPF3 intron (GRCh38 / hg38:chr1 150325882 150328319); PRPF3 intron (GRCh38 / hg38:chr1 150328467 150332683); SCN2A intron (GRCh38 / hg38:chr2 165326985 165331329); SCN8A intron (GRCh38 / hg38:chr12 51687220 51689004); SCN8A intron (GRCh38 / hg38:chr12 51774363 51786541); intron of SCN9A (GRCh38 / hg38:chr2 166304122 166305791); intron of SEMA3C (GRCh38 / hg38:chr7 80789529 80798091); intron of SEMA3D (GRCh38 / hg38:chr7 85055860 85065423); intron of SIRT3 (GRCh38 / hg38:chr11 224241 230451); intron of STK11 (GRCh38 / hg38:chr19 1207204 1218416); intron of STK11 (GRCh38 / hg38:chr19 1221341 1221948); intron of SYNGAP1 (GRCh38 / hg38:chr6 33447934 33451759); intron of TOPORS (GRCh38 / hg38:chr9 32550969 32552433); or intron of VCAN (GRCh38 / hg38:chr5 83542269 83545536).

[0056]

[0140] In some embodiments, the methods and compositions of the disclosure are directed to the expression of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB , PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AK T3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 By inducing exon skipping of pseudoexons in NIE-containing pre-mRNAs, ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2 , MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, S LC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3 In some embodiments, the pseudoexon is a sequence within any of introns 1 to 50. In some embodiments, the pseudoexon is a sequence within any of introns 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50. In some embodiments, the pseudoexon is any of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1 , PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 intron or a portion thereof. In some embodiments, the pseudoexon is intron 8 of ABCB4, intron 9 of ASS1, intron 16 of ATP8B1, intron 1 of BAG3, intron 31 of CACNA1A, intron 36 of CACNA1A, intron 37 of CACNA1A, intron 3 of CBS, intron 12 of CBS, intron 1 of CD55, intron 16 of CDKL5, intron 3 of CFH, intron 30 of CHD2,Intron 4 of CHRNA7, intron 1 of CISD2, intron 15 of CLN3, intron 11 of COL4A3, intron 41 of COL4A3, intron 22 of COL4A4, intron 44 of COL4A4, intron 20 of DEPDC5, intron 2 of DHDDS, intron 3 of ELOVL4, intron 5 of FAH, intron 4 of FN, intron 4 of GALE, intron 3 of GBE1, intron 11 of GRIN2A, GRN intron 1 of HEA, intron 2 of KANSL1, intron 2 of KMT2D, intron 50 of KMT2D, intron 8 of MAPK3, intron 13 of MBD5, intron 2 of MECP2, intron 11 of MUT, intron 31 of NF1, intron 7 of NIPBL, intron 38 of NIPBL, intron 11 of NSD1, intron 6 of OPA1, intron 28 of OPA1, intron 1 of OPTN, intron 1 of PCCA, intron 2 of PCCB intron 5 of PCCB, intron 6 of PKP2, intron 23 of PLCB1, intron 3 of PRPF3, intron 9 of PRPF31, intron 1 of RAI1, intron 5 of RBFO2, intron 13 of SCN2A, intron 6 of SCN3A, intron 7 of SCN3A, intron 4 of SCN8A, intron 6 of SCN8A, intron 20 of SCN9A, intron 24 of SHANK3, S In some embodiments, the pseudoexon is within intron 3 of LC25A13, intron 6 of SLC25A13, intron 9 of SLC25A13, intron 11 of SLC25A13, intron 13 of SLC25A13, intron 1 of SLC6A1, intron 12 of SPTAN1, intron 10 of TEK, intron 15 of TEK, intron 1 of TOPORS, intron 11 of TSC2, intron 30 of TSC2, intron 1 of UBE3A, or intron 7 of VCAN.AKT3 intron (GRCh38 / hg38:chr1 243563849 243572925); CACNA1A intron (GRCh38 / hg38:chr19 13235731 13241520); CBS intron (GRCh38 / hg38:chr21 43059304 43060440); CD46 intron (GRCh38 / , hg38:chr1 207770363 207783291; CFH intron (GRCh38 / hg38:chr1 196673963 196675988); CHD2 intron (GRCh38 / hg38:chr15 92997404 92998498); CLN3 intron (GRCh38 / hg38:chr16 28477878 28482104); COL11A2 intron (GRCh38 / hg38:chr6 33181172 33184144); COL4A3 intron (GRCh38 / hg38:chr2 227295317 227297673; COL4A4 intron (GRCh38 / hg38:chr2 227144559 227147412); COL4A4 intron (GRCh38 / hg38:chr2 227012299 227022047); CR1 intron (GRCh38 / hg38:chr1 207630622 207639396); CRX intron (GRCh38 / hg38:chr19 47834544 47836242); CYP2J2 intron (GRCh38 / hg38:chr1 59901104 59904870); DHDDS intron (GRCh38 / hg38:chr1 26438285 26442730); intron of DNAJC8 (GRCh38 / hg38:chr1 28229025 28232920); intron of EIF2AK3 (GRCh38 / hg38:chr2 88579641 88583429); intron of ERN1 (GRCh38 / hg38:chr17 64098242 64129975); intron of GALE (GRCh38 / hg38:chr1 23798231 23798614); intron of GUCY2F (GRCh38 / hg38:chrx 109382213 109385183); intron of GUCY2F (GRCh38 / hg38:chrx 109430397 109441350); HEXA intron (GRCh38 / hg38:chr15 72356651 72375719); HEXA intron (GRCh38 / hg38:chr15 72345552 72346234); MAPK3 intron (GRCh38 / hg38:chr16 30114709). 30116635); intron of MBD5 (GRCh38 / hg38:chr2 148458872 148462581); intron of MBD5 (GRCh38 / hg38:chr2 148490595 148502435); intron of MBD5 (GRCh38 / hg38:chr2 148502510 148510059); intron of MUT (GRCh38 / hg38:chr6 49435625 49440205); intron of MYH14 (GRCh38 / hg38:chr19 50230624 50231929); intron of MYO6 (GRCh38 / hg38:chr6 75867106 75870646; NF1 intron (GRCh38 / hg38:chr17 31249120 31252937); NF2 intron (GRCh38 / hg38:chr22 29604113 29636750); NIPBL intron (GRCh38 / hg38:chr5 37046200 37048501); NR1H4 intron (GRCh38 / hg38:chr12 100493403 100505574); NSD1 intron (GRCh38 / hg38:chr5 177136031 177191883); NSD1 intron (GRCh38 / hg38:chr5 177192020 177204119); NSD1 intron (GRCh38 / hg38:chr5 177246797 177248180); NSD1 intron (GRCh38 / hg38:chr5 177273785 177280564); OPA1 intron (GRCh38 / hg38:chr3 193626203 193631611); OPA1 intron (GRCh38 / hg38:chr3 193593374 193614710); PCCA intron (GRCh38 / hg38:chr13 100302999 100307191); PKP2 intron (GRCh38 / hg38:chr12 32879033 32896508); PPARA intron (GRCh38 / hg38:chr22 46198592 46215172); PRPF3 intron (GRCh38 / hg38:chr1 150325882 150328319); PRPF3 intron (GRCh 38 / hg38:chr1 150328467 150332683); intron of SCN2A (GRCh38 / hg38:chr2 165326985 165331329); intron of SCN8A (GRCh38 / hg38:chr12 51687220 51689004); intron of SCN8A (GRCh38 / hg38:chr12 51774363 51786541); intron of SCN9A (GRCh38 / hg38:chr2 166304122 166305791; SEMA3C intron (GRCh38 / hg38:chr7 80789529 80798091); SEMA3D intron (GRCh38 / hg38:chr7 85055860 85065423); SIRT3 intron (GRCh38 / hg38:chr11 224241 230451); STK11 intron (GRCh38 / hg38:chr19 1207204 1218416); STK11 intron (GRCh38 / hg38:chr19 1221341 1221948); SYNGAP1 intron (GRCh38 / hg38:chr6 33447934 33451759); within an intron of TOPORS (GRCh38 / hg38:chr9 32550969 32552433); or within an intron of VCAN (GRCh38 / hg38:chr5 83542269 83545536). Protein expression

[0141] In some embodiments, the methods described herein provide for the functionalization of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, P Used to increase production of RPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein or RNA.As used herein, the term "functional" refers to the condition or disease being treated, e.g., Alport syndrome; amyotrophic lateral sclerosis (ALS); Angelman syndrome; primary progressive aphasia; arrhythmogenic right ventricular dysplasia; autism spectrum disorder; dilated cardiomyopathy; myofibrillar myopathy; neuronal ceroid lipofuscinosis; intrahepatic cholestasis of pregnancy; progressive familial intrahepatic cholestasis; citrullinemia type II; citrullinemia type 1; cognitive impairment with or without cerebral ataxia; Cornelia de Lange; early-onset epileptic encephalopathy; epilepsy-aphasia spectrum disorder. Ram; generalized epilepsy with febrile convulsions plus type 7; childhood-onset epileptic encephalopathy; early infantile epileptic encephalopathy 11; early infantile epileptic encephalopathy 12; early infantile epileptic encephalopathy 13; early infantile epileptic encephalopathy 2; paroxysmal ataxia type 2; familial focal epilepsy; familial febrile convulsions 3B; Friedreich's ataxia; Friedreich's ataxia with preserved reflexes; galactose epimerase deficiency; primary congenital glaucoma 3E; glycogen storage disease IV; GRN-related frontotemporal dementia; B6-responsive and non-responsive homocystinuria; autosomal recessive HSAN2D; congenital insensitivity to pain; Kabuki syndrome; Koolen-De Vries Vries syndrome; autosomal dominant mental retardation 1; methylmalonic aciduria; familial hemiplegic migraine 1; myoclonic atonic epilepsy; neurofibromatosis type 1; opioid dependence; optic atrophy type 1; Phelan-McDermid syndrome; propionic acidemia; primary open-angle glaucoma; propionic academia; retinitis pigmentosa 11; retinitis pigmentosa 18; retinitis pigmentosa 31; retinitis pigmentosa 59. ;Rett syndrome;Benign familial infantile seizures 3;Benign familial infantile seizures 5;Smith-Magenis syndrome;Sotos syndrome 1;Beckwith-Wiedemann syndrome;Stargardt disease 3;Tay-Sachs disease;Tuberous sclerosis complex;Tyrosinemia type I;Wagner syndrome 1;West syndrome;Wolfram syndrome 2 / NAFLD;15q13.3 microdeletion;16p11.2 deletion syndrome;Autosomal dominant hearing loss 13;Cone-rod retinal dystrophy 2;Autosomal ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDD required to eliminate one or more of the following symptoms: somatic dominant hearing loss 4A; peripheral neuropathy, myopathy, hoarseness, and hearing loss; autosomal dominant hearing loss 22; neurofibromatosis type 2; NASH; or autosomal dominant mental retardation 5 S, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NS D1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A 13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein or RNA activity or function.In some embodiments, the method comprises administering to a patient a partially functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3 , PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein or RNA production.As used herein, the term "partial functionality" refers to an activity or function of a gene that is less than the amount of activity or function required to eliminate or prevent any one or more symptoms of a disease or condition, such as ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, or the like. Refers to any amount of OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein or RNA activity or function. In some embodiments, the partially functional protein or RNA has at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% less activity than the fully functional protein or RNA. It can have a sexual nature.

[0057]

[0142] In some embodiments, the method comprises administering to the patient an effective amount of an inhibitor of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, have NIE-containing mRNA precursors encoding PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 proteins ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GA by target cells LE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RA 1. A method for increasing expression of I1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein, wherein the subject isATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, Defective levels of RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein activity Alport syndrome caused by amyotrophic lateral sclerosis (ALS); Angelman syndrome; primary progressive aphasia; arrhythmogenic right ventricular dysplasia (9); autism spectrum disorder; dilated cardiomyopathy (1HH); myofibrillar myopathy (6); neuronal ceroid lipofuscinosis (3); intrahepatic cholestasis of pregnancy (3); progressive familial intrahepatic cholestasis (1); citrullinemia type II; citrullinemia type 1; cognitive impairment with or without cerebral ataxia; Cornelia de Lange syndrome; early-onset epileptic encephalopathy; epilepsy. Aphasia spectrum; generalized epilepsy with febrile convulsions plus type 7; childhood-onset epileptic encephalopathy; early infantile epileptic encephalopathy 11; early infantile epileptic encephalopathy 12; early infantile epileptic encephalopathy 13; early infantile epileptic encephalopathy 2; paroxysmal ataxia type 2; familial focal epilepsy; familial febrile convulsions 3B; Friedreich's ataxia; Friedreich's ataxia with preserved reflexes; galactose epimerase deficiency; primary congenital glaucoma 3E; glycogen storage disease IV; GRN-related frontotemporal dementia; B6-reactive and non-reactive homocystinuria; autosomal, Chromosome recessive HSAN2D; congenital insensitivity to pain; Kabuki syndrome; Koolen-De Vries syndrome; autosomal dominant mental retardation 1; methylmalonic aciduria; familial hemiplegic migraine 1; myoclonic atonic epilepsy; neurofibromatosis type 1; opioid dependence; optic atrophy type 1; Phelan-McDermid syndrome; propionic acidemia; primary open-angle glaucoma; propionic acidemia academia); retinitis pigmentosa 11; retinitis pigmentosa 18; retinitis pigmentosa 31; retinitis pigmentosa 59; Rett syndrome; benign familial infantile seizures 3; benign familial infantile seizures 5; Smith-Magenis syndrome; Sotos syndrome 1; Beckwith-Wiedemann syndrome; Stargardt disease 3; Tay-Sachs disease; tuberous sclerosis complex; tyrosinemia type 1; Wagner syndrome 1; West syndrome; Wolfram syndrome 2 / NAFLD; 15q13.3 microdeletion; 16p11 .2 deletion syndrome; autosomal dominant hearing loss 13; cone-rod retinal dystrophy 2; autosomal dominant hearing loss 4A; peripheral neuropathy, myopathy, hoarseness, and hearing loss; autosomal dominant hearing loss 22; neurofibromatosis type 2; NASH; or autosomal dominant mental retardation 5 and have ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1 , SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein deficiency is associated with ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS,CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL 1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A It is caused by haploinsufficiency of SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 proteins. In such embodiments, the subject has a functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN The first allele encoding 2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein, and the second allele encoding ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2,CHRNA 7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK 3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A , SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein is not produced.In another such embodiment, the subject has a functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, M ECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MY A first allele encoding H14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein and a non-functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL 4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SH. and having a second allele encoding an ANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein. In another such embodiment, the subject has a gene encoding a gene encoding a functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF4, PRPF5, PRPF6, PRPF7, PRPF8, PRPF9, PRPF10, PRPF11, PRPF12, PRPF13, PRPF14, PRPF15, PRPF16, PRPF17, PRPF18, PRPF19, PRPF20, PRPF21, PRPF22, PRPF23, PRPF24, PRPF25, PRPF26, PRPF27, PRPF28, PRPF39, PRPF40, PRPF51, PRPF52, PRPF53, PRPF64, PRPF75, PRPF81, PRPF92, PRPF19, PRPF16, PRPF18, PRPF19, PRPF29, PRPF20, PRPF21, PRPF22, PRPF25, PRPF26, PRPF28, PRPF29, PRPF30, PRPF41, PRPF52, PRPF53, PRPF64, PRPF75, PRPF81, PRPF92, PRPF15, PRPF16, PRPF17, PRPF18, PRPF19, PRPF21, PRPF22, PRPF23, PRPF24, PRPF 31, first alleles encoding RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 proteins, and partially functional ABCB4, ASS1, ATP8 B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2 A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, R and having a second allele encoding a BFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein. In any of these embodiments, the antisense oligomer binds to a targeted portion of the NIE-containing pre-mRNA transcribed from the second allele, thereby inducing exon skipping of the pseudoexon from the pre-mRNA and inhibiting the expression of a functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, S LC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4,Increased levels of mature mRNA encoding STK11, PPARA, CYP2J2, or SYNGAP1 proteins, and increased levels of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPT in cells of the subject N, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein expression.

[0058]

[0143] In some embodiments, the method comprises administering to the patient a therapeutically effective amount of a medicament comprising ... F1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK 3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2 , ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEX by subject cells harboring NIE-containing mRNA precursors encoding SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 proteins. A, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, S 1. A method for increasing expression of an EMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein, wherein the subject is D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1,Alport syndrome caused by deficient amounts of GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein activity; amyotrophic lateral sclerosis (ALS); Angelman syndrome; primary progressive aphasia; arrhythmogenic right ventricular dysplasia 9; autism spectrum disorder; dilated cardiomyopathy 1HH; myofibrillar myopathy 6; neuronal ceroid lipofuscinosis 3; intrahepatic cholestasis of pregnancy 3; progressive familial intrahepatic cholestasis 1; citrullinemia type II; citrullinemia type 1; cognitive impairment with or without cerebral ataxia; Cornelia de Lange syndrome; early-onset epilepsy Encephalopathy; Epilepsy-Aphasia Spectrum; Generalized Epilepsy with Febrile Convulsions Plus Type 7; Childhood-Onset Epileptic Encephalopathy; Early Infantile Epileptic Encephalopathy Type 11; Early Infantile Epileptic Encephalopathy Type 12; Early Infantile Epileptic Encephalopathy Type 13; Early Infantile Epileptic Encephalopathy Type 2; Paroxysmal Ataxia Type 2; Familial Focal Epilepsy; Familial Febrile Convulsions Type 3B; Friedreich's Ataxia; Friedreich's Ataxia with Preserved Reflexes; Galactose Epimerase Deficiency; Primary Congenital Glaucoma Type 3E; Glycogen Storage Disease Type IV; GRN-Related Frontotemporal Dementia; B6-Responsive and Non-Responsive Homocystinuria; Autosomal Recessive HSAN2D; Congenital Insensitivity to Pain; Kabuki Syndrome; Koolen-De Vries Vries syndrome; autosomal dominant mental retardation 1; methylmalonic aciduria; familial hemiplegic migraine 1; myoclonic atonic epilepsy; neurofibromatosis type 1; opioid dependence; optic atrophy type 1; Phelan-McDermid syndrome; propionic acidemia; primary open-angle glaucoma; propionic acidemia academia); retinitis pigmentosa 11; retinitis pigmentosa 18; retinitis pigmentosa 31; retinitis pigmentosa 59; Rett syndrome; benign familial infantile seizures 3; benign familial infantile seizures 5; Smith-Magenis syndrome; Sotos syndrome 1; Beckwith-Wiedemann syndrome; Stargardt disease 3; Tay-Sachs disease; tuberous sclerosis; tyrosinemia type 1; Wagner syndrome 1; West syndrome; Wolfram syndrome 2 / NAFLD; 15q13.3 microdeletion; 16p11.2 deletion syndrome; autosomal dominant hearing loss 13; cone-rod retinal dystrophy 2; autosomal dominant hearing loss 4A; peripheral neuropathy, myopathy, hoarseness, and hearing loss; autosomal dominant hearing loss 22; neurofibromatosis type 2; NASH; also had autosomal dominant mental retardation 5 and was associated with ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PR Defective amounts of PF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein are inherited in an autosomal recessive manner.

[0059]

[0144] In some embodiments, the method comprises administering to the patient an effective amount of an inhibitor of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, have NIE-containing mRNA precursors encoding PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 proteins ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GA by target cells LE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RA 1. A method for increasing expression of I1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein, wherein the subject isATP8B1、BAG3、CACNA1A、CBS、CD55、CDKL5、CFH、CHD2、CHRNA7、CIS D2、CLN3、COL4A3、COL4A4、DEPDC5、DHDDS、ELOVL4、FAH、FXN、GALE、 GBE1、GRIN2A、GRN、HEXA、KANSL1、KCNQ2、KMT2D、MAPK3、MBD5、MECP 2、MUT、NF1、NIPBL、NSD1、OPA1、OPTN、PCCA、PCCB、PKP2、PLCB1、PRP F3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, C D46、COL11A2、CR1、CRX、DNAJC8、MYH14、MYO6、NF2、SEMA3C、SEMA3D 、EIF2AK3、ERN1、GUCY2F、SIRT3、NR1H4、STK11、PPARA、CYP2J2、また、 Alport syndrome, caused by deficient amounts of SYNGAP1 protein activity; amyotrophic lateral sclerosis (ALS); Angelman syndrome; primary progressive aphasia; arrhythmogenic right ventricular dysplasia (RBD); autism spectrum disorder (ASD); dilated cardiomyopathy (DCM); myofibrillar myopathy (MM); neuronal ceroid lipofuscinosis (CERI); intrahepatic cholestasis of pregnancy (ICP); progressive familial intrahepatic cholestasis (IIP); citrullinemia type II; citrullinemia type 1; cognitive impairment with or without cerebral ataxia; Cornelia de Lange syndrome; early-onset epileptic encephalopathy; epilepsy-aphasia spectrum disorder; general Epileptic febrile convulsions plus type 7; childhood-onset epileptic encephalopathy; early infantile epileptic encephalopathy 11; early infantile epileptic encephalopathy 12; early infantile epileptic encephalopathy 13; early infantile epileptic encephalopathy 2; paroxysmal ataxia type 2; familial focal epilepsy; familial febrile convulsions 3B; Friedreich's ataxia; Friedreich's ataxia with preserved reflexes; galactose epimerase deficiency; primary congenital glaucoma 3E; glycogen storage disease IV; GRN-related frontotemporal dementia; B6-responsive and non-responsive homocystinuria; autosomal recessive HSAN2D; congenital insensitivity to pain; Kabuki syndrome; Koolen-De Vries Vries syndrome; autosomal dominant mental retardation 1; methylmalonic aciduria; familial hemiplegic migraine 1; myoclonic atonic epilepsy; neurofibromatosis type 1; opioid dependence; optic atrophy type 1; Phelan-McDermid syndrome; propionic acidemia; primary open-angle glaucoma; propionic acidemia; retinitis pigmentosa 11; retinitis pigmentosa 18; retinitis pigmentosa 31; retinitis pigmentosa 59; Rett syndrome; benign familial infantile seizures 3; benign familial infantile seizures 5; Smith-Magenis syndrome; Sotos syndrome 1; Beckwith-Wiedemann syndrome; Stargardt disease 3; Tay-Sachs disease; tuberous sclerosis complex; tyrosinemia type 1; Wagner syndrome 1; West syndrome; Wolfram syndrome 2 / NAFLD; 15q13.3 microdeletion; 16p11.2 deletion syndrome; autosomal dominant hearing loss 13; cone-rod retinal dystrophy 2; autosomal dominant hearing loss 4A; peripheral neuropathy, myopathy, hoarseness, and hearing loss; autosomal dominant hearing loss 22; neurofibromatosis type 2; NASH; or autosomal dominant mental retardation 5, and have ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPB Deficient amounts of L, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein are inherited in an autosomal dominant manner.

[0060]

[0145] In some embodiments, the method comprises administering to the patient a therapeutically effective amount of a medicament for treating or preventing the onset of inflammatory bowel disease, including ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, P LCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP by subject cells with NIE-containing precursor mRNAs encoding 2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein expression The method, wherein the subject is a patient with any of the following: ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF4, PRPF5, PRPF6, PRPF7, PRPF8, PRPF9, PRPF10, PRPF11, PRPF12, PRPF13, PRPF14, PRPF15, PRPF16, PRPF17, PRPF18, PRPF19, PRPF20, PRPF21, PRPF22, PRPF23, PRPF24, PRPF25, PRPF26, PRPF27, PRPF28, PRPF29, PRPF30, PRPF31, PRPF32, PRPF33, PRPF35, PRPF36, PRPF37, PRPF38, PRPF39, PRPF40, PRPF41, PRPF42, PRPF43, PRPF45, PRPF46, PRPF47, PRPF48, PRPF49, PRPF50, PRPF51, PRPF52, PRPF53, PRPF54, PRPF55, PRPF56, PRPF57, PRPF58, PRPF59, PRPF61, PRPF62, PRPF63, PRPF64, PRPF65, PRPF66, PRPF67, PRPF68, PRPF69, PRPF7 Alport syndrome, caused by deficient amounts of RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein activity;Amyotrophic lateral sclerosis (ALS); Angelman syndrome; primary progressive aphasia; arrhythmogenic right ventricular dysplasia 9; autism spectrum disorder; dilated cardiomyopathy 1HH; myofibrillar myopathy 6; neuronal ceroid lipofuscinosis 3; intrahepatic cholestasis of pregnancy 3; progressive familial intrahepatic cholestasis 1; citrullinemia type II; citrullinemia type 1; cognitive impairment with or without cerebral ataxia; Cornelia de Lange; early-onset epileptic encephalopathy; epilepsy-aphasia spectrum disorder; generalized epilepsy with febrile convulsions plus type 7; childhood-onset Epileptic encephalopathy; early infantile epileptic encephalopathy 11; early infantile epileptic encephalopathy 12; early infantile epileptic encephalopathy 13; early infantile epileptic encephalopathy 2; paroxysmal ataxia type 2; familial focal epilepsy; familial febrile convulsions 3B; Friedreich's ataxia; Friedreich's ataxia with preserved reflexes; galactose epimerase deficiency; primary congenital glaucoma 3E; glycogen storage disease IV; GRN-related frontotemporal dementia; B6-responsive and non-responsive homocystinuria; autosomal recessive HSAN2D; congenital insensitivity to pain; Kabuki syndrome; Koolen-De Vries Vries syndrome; autosomal dominant mental retardation 1; methylmalonic aciduria; familial hemiplegic migraine 1; myoclonic atonic epilepsy; neurofibromatosis type 1; opioid dependence; optic atrophy type 1; Phelan-McDermid syndrome; propionic acidemia; primary open-angle glaucoma; propionic acidemia; retinitis pigmentosa 11; retinitis pigmentosa 18; retinitis pigmentosa 31; retinitis pigmentosa 59; Rett syndrome; benign familial infantile seizures 3; benign familial infantile seizures 5; Smith-Magenis syndrome; Sotos syndrome 1; Beckwith-Wiedemann syndrome; Stargardt disease 3; Tay-Sachs disease; tuberous sclerosis complex; tyrosinemia type 1; Wagner syndrome 1; West syndrome; Wolfram syndrome 2 / NAFLD; 15q 13.3 microdeletion; 16p11.2 deletion syndrome; autosomal dominant hearing loss 13; cone-rod retinal dystrophy 2; autosomal dominant hearing loss 4A; peripheral neuropathy, myopathy, hoarseness, and hearing loss; autosomal dominant hearing loss 22; neurofibromatosis type 2; NASH; or autosomal dominant mental retardation 5, with ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CI; SD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD 5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A Defective amounts of SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 proteins are inherited in an X-linked dominant manner.

[0061]

[0146] In a related embodiment, the method is a method of increasing the expression of a protein or functional RNA using an ASO. In some embodiments, the ASO is selected from the group consisting of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PK P2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT 3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGA ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, O in cells of subjects with NIE-containing mRNA precursors encoding P1 proteins PA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPOR S, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11,The present invention can be used to increase the expression of PPARA, CYP2J2, or SYNGAP1 proteins, and the subject can be administered a combination of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein levels Defects in function, e.g., Alport syndrome; amyotrophic lateral sclerosis (ALS); Angelman syndrome; primary progressive aphasia; arrhythmogenic right ventricular dysplasia; autism spectrum disorder; dilated cardiomyopathy; myofibrillar myopathy; neuronal ceroid lipofuscinosis; intrahepatic cholestasis of pregnancy; progressive familial intrahepatic cholestasis; citrullinemia type II; citrullinemia type 1; cognitive impairment with or without cerebral ataxia; Cornelia de Lange syndrome; early-onset epileptic encephalopathy; epilepsy-aphasia spectrum disorder; generalized epilepsy; febrile convulsions Plus type 7; childhood-onset epileptic encephalopathy; early infantile epileptic encephalopathy 11; early infantile epileptic encephalopathy 12; early infantile epileptic encephalopathy 13; early infantile epileptic encephalopathy 2; paroxysmal ataxia type 2; familial focal epilepsy; familial febrile convulsions 3B; Friedreich's ataxia; Friedreich's ataxia with preserved reflexes; galactose epimerase deficiency; primary congenital glaucoma 3E; glycogen storage disease IV; GRN-related frontotemporal dementia; B6-responsive and non-responsive homocystinuria; autosomal recessive HSAN2D; congenital insensitivity to pain; Kabuki syndrome; Koolen-De Vries Vries syndrome; autosomal dominant mental retardation 1; methylmalonic aciduria; familial hemiplegic migraine 1; myoclonic atonic epilepsy; neurofibromatosis type 1; opioid dependence; optic atrophy type 1; Phelan-McDermid syndrome; propionic acidemia; primary open-angle glaucoma; propionic acidemia academia); retinitis pigmentosa 11; retinitis pigmentosa 18; retinitis pigmentosa 31; retinitis pigmentosa 59; Rett syndrome; benign familial infantile seizures 3; benign familial infantile seizures 5; Smith-Magenis syndrome; Sotos syndrome 1; Beckwith-Wiedemann syndrome; Stargardt disease 3; Tay-Sachs disease; tuberous sclerosis; tyrosinemia type 1; Wagner syndrome 1; West syndrome; Wolfram syndrome 2 / NAFLD; 15q13.3 microdeletion; 16p11.2 deletion syndrome; autosomal dominant hearing loss 13; cone-rod retinal dystrophy 2; autosomal dominant hearing loss 4A; peripheral neuropathy, myopathy, hoarseness, and hearing loss; autosomal dominant hearing loss 22; neurofibromatosis type 2; NASH; or autosomal dominant mental retardation 5.

[0062]

[0147] In some embodiments, NIE-containing pre-mRNA transcripts encoding proteins that cause a disease or condition are targeted by the ASOs described herein. In some embodiments, NIE-containing pre-mRNA transcripts encoding proteins that do not cause the disease are targeted by the ASOs. For example, a disease resulting from a mutation or deficiency of a first protein in a specific pathway can be ameliorated by targeting an NIE-containing pre-mRNA encoding a second protein, thereby increasing production of the second protein. In some embodiments, the function of the second protein can compensate for the mutation or deficiency of the first protein (which causes the disease or condition).

[0063]

[0148] In some embodiments, the subject: (a)(i)ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE , GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1 RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein is produced at reduced levels compared to production from the wild-type allele. (ii) ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, C D55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ 2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A , SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein is produced in a form that has reduced function compared to the equivalent wild-type protein; or (iii) ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, G ALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF 31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein or functional RNA is not produced the first mutant allele, and (b)(i)ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE , GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1 RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein is produced at reduced levels compared to production from the wild-type allele. (ii) ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4 , FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3 A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPA the RA, CYP2J2, or SYNGAP1 protein is produced in a form that has reduced functionality compared to the equivalent wild-type protein, or (iii) ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FX N, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3 , PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein is not produced Second mutant allele and the NIE-containing pre-mRNA is transcribed from a first allele and / or a second allele. In these embodiments, the ASO binds to a targeting portion of the NIE-containing pre-mRNA transcribed from the first allele or the second allele, thereby inducing exon skipping of the pseudoexon from the NIE-containing pre-mRNA, and is capable of targeting a gene encoding one of the following: ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PC increasing the level of mRNA encoding a CA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein, and increasing expression of the target protein or functional RNA in cells of the subject. In these embodiments, the target protein or functional RNA having increased expression levels resulting from exon skipping of the pseudoexon from the NIE-containing pre-mRNA may be in a form that has reduced functionality (partial functionality) compared to the equivalent wild-type protein, or in a form that has complete functionality (full functionality) compared to the equivalent wild-type protein.

[0064]

[0149] In some embodiments, ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, R The levels of mRNA encoding BFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein are measured in control cells, e.g., treated with antisense oligomers. Specifically, ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, and CFH CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4 FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3 MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLC B1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3 SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD 46. ​​COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF 2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, and SYNGAP1ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP produced in cells treated with antisense oligomers that do not bind to the targeted portion of the NIE-containing pre-mRNA 2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein, is increased by 1.1 to 10-fold compared to the amount of mRNA encoding these proteins.

[0065]

[0150] In some embodiments, subjects treated using the methods of the present disclosure have one allele to partial functionality of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1 , NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1 , SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2 F, expressing SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 proteins and partially functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SL C25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2A K3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein may be caused by frameshift mutation, nonsense mutation, missense mutation, or partial gene deletion. In some embodiments, the subject treated using the method of the present disclosure has one allele to non-functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25 A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2 expressing AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 proteins and non-functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KC NQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN 3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14,The MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 proteins can be caused by frameshift mutations, nonsense mutations, missense mutations, or partial gene deletions in one allele. In some embodiments, the subject being treated using the methods of the present disclosure has one or more of the following mutations at one allele: ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, P CCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 whole-gene deletion. Exon inclusion

[0151] As used herein, an "NIE-containing pre-mRNA" is a pre-mRNA transcript that contains at least one pseudoexon. Alternative or aberrant splicing can result in the inclusion of at least one pseudoexon in a mature mRNA transcript. The terms "mature mRNA" and "fully spliced ​​mRNA" are used interchangeably herein to refer to a fully processed mRNA. The inclusion of at least one pseudoexon can result in a non-productive mRNA, leading to NMD of the mature mRNA. NIE-containing mature mRNAs can sometimes result in aberrant protein expression.

[0066]

[0152] In some embodiments, the included pseudoexon is the most abundant pseudoexon in a population of NIE-containing pre-mRNAs transcribed from a gene encoding a target protein in a cell. In some embodiments, the included pseudoexon is the most abundant pseudoexon in a population of NIE-containing pre-mRNAs transcribed from a gene encoding a target protein in a cell, and the population of NIE-containing pre-mRNAs contains two or more included pseudoexons. In some embodiments, an antisense oligomer targeted to the most abundant pseudoexon in a population of NIE-containing pre-mRNAs encoding a target protein induces exon skipping of one or more pseudoexons in the population, including the pseudoexon targeted or bound by the antisense oligomer. In some embodiments, the targeting region is selected from the group consisting of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, The most abundant pseudoexons are found in NIE-containing pre-mRNAs encoding RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 proteins.

[0067]

[0153] The degree of exon inclusion can be expressed as the exon inclusion rate, e.g., the percentage of transcripts that include a given pseudoexon. Briefly, the exon inclusion rate can be calculated as the percentage of the amount of RNA transcripts with exon inclusion relative to the sum of the average amount of RNA transcripts with exon inclusion and the average amount of RNA transcripts with exon exclusion.

[0068]

[0154] In some embodiments, an included pseudoexon is an exon identified as an included pseudoexon based on a determination of an inclusion rate of at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, or at least about 50%. In several embodiments, an included pseudoexon is an exon that is identified as an included pseudoexon based on a determination of an inclusion rate of at least about 5% to about 100%, at least about 5% to about 95%, at least about 5% to about 90%, at least about 5% to about 85%, at least about 5% to about 80%, at least about 5% to about 75%, at least about 5% to about 70%, at least about 5% to about 65%, at least about 5% to about 60%, at least about 5% to about 55%, at least about 5% to about 50%, at least about 5% to about 45%, at least about 5% to about 40%. 0%, about 5% to about 35%, about 5% to about 30%, about 5% to about 25%, about 5% to about 20%, about 5% to about 15%, about 10% to about 100%, about 10% to about 95%, about 10% to about 90%, about 10% to about 85%, about 10% to about 80%, about 10% to about 75%, about 10% to about 70%, about 10% to about 65%, about 10% to about 60%, about 10% to about 55%, about 10% to about 50%, about 10% to about 45%, about 10% to about 40%, about 10% to about 35%, about 10% to about 30%, about 10% to about 25%, about 10% to about 20%, about 15% to about 100%, about 15% to about 95%, about 15% to about 90%, about 15% to about 85%, about 15% to about 80%, about 15% to about 75%, about 15% to about 70%, about 15% to about 65%, about 15% to about 60%, about 15% to about 55%, about 15% to about 50%, about 15% to about 45%, about 15% to about 40%, about 15% to about 35%, about 15% to about 30%, about 15% to about 25%, about 20% to about 100%, about 20% to about 95%, about 20% to About 90%, about 20% to about 85%, about 20% to about 80%, about 20% to about 75%, about 20% to about 70%, about 20% to about 65%, about 20% to about 60%, about 20% to about 55%, about 20% to about 50%, about 20% to about 45%, about 20% to about 40%, about 20% to about 35%, about 20% to about 30%, about 25% to about 100%, about 25% to about 95%, about 25% to An exon is identified as an inclusion pseudoexon based on a determination of an inclusion rate of about 90%, about 25% to about 85%, about 25% to about 80%, about 25% to about 75%, about 25% to about 70%, about 25% to about 65%, about 25% to about 60%, about 25% to about 55%, about 25% to about 50%, about 25% to about 45%, about 25% to about 40%, or about 25% to about 35%. ENCODE data (e.g., Tilgner et al., 2012, "Deep sequencing of subcellular RNA fractions shows splicing to be predominantly "Co-transcriptional in the human genome but inefficient for lncRNAs," Genome Research 22(9):1616-25) can be used to assist in identifying exon inclusion.

[0069]

[0155] Other genes include ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, and CDKL5. CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL 4. FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAP K3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, P.S LCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHAN K3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, C.S D46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EI F2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, and SYNGAP1Cells contacted with an ASO that is complementary to a targeted portion of a pre-mRNA transcript produce at least 10, 20, 30, 40, 50, 60, 80, 100, 150, 200, 250, 300, 350, 400, 450, 500, or 1000% more of the following proteins compared to the amount produced by the cells in the absence / absence of ASO / treatment: ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D , MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein levels. In some embodiments, the antisense oligomer is produced by a cell contacted with an antisense oligomer, and the antisense oligomer is selected from the group consisting of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCC B, the total amount of PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein is about 20% to about 300%, about 50% to about 300%, compared to the amount of target protein produced by a control compound. , about 100% to about 300%, about 150% to about 300%, about 20% to about 50%, about 20% to about 100%, about 20% to about 150%, about 20% to about 200%, about 20% to about 250%, about 50% to about 100%, about 50% to about 150%, about 50% to about 200%, about 50% to about 250%, about 100 to about 150%, about 100% to about 200%, about 100% to about 250%, about 150% to about 200%, about 150% to about 250%, about 200% to about 250%, at least about 10%, at least about 20%, at least about 50%, at least about 100%, at least about 150%, at least about 200%, at least about 250%, or at least about 300% increase.In some embodiments, the antisense oligomer is produced by a cell contacted with an antisense oligomer that inhibits ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, M BD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MY The total amount of O6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein is increased by about 1.1 to about 10 times, about 1.5 to about 10 times, about 2 to about 10 times, about 3 to about 10 times, about 4 to about 10 times, about 1.1 to about 5 times, about 1.1 to about 6 times, about 1.1 to about 7 times, about 1.1 to about 8 times, about 1.1 to about 9 times, about 1.1 to about 10 times, about 1.1 to about 11 times, about 1.1 to about 12 times, about 1.1 to about 13 times, about 1.1 to about 14 times, about 1.1 to about 15 times, about 1.1 to about 16 times, about 1.1 to about 17 times, about 1.1 to about 18 times, about 1.1 to about 19 times, about 1.1 to about 20 times, about 1.1 to about 21 times, about 1.1 to about 22 times, about 1.1 to about 23 times, about 1.1 to about 24 times, about 1.1 to about 25 times, about 1.1 to about 26 times, about 1.1 to about 27 times, about 1.1 to about 28 times, about 1.1 to about 29 times, about 2.1 to about 30 times, about 1.1 to about 31 times, about 1.1 to about 32 times, about 1.1 to about 33 times, about 1.1 to about 34 times, about 1.1 to about 35 times, about 1.1 to about 36 times, about 1. an increase of about 8-fold, about 1.1 to about 9-fold, about 2 to about 5-fold, about 2 to about 6-fold, about 2 to about 7-fold, about 2 to about 8-fold, about 2 to about 9-fold, about 3 to about 6-fold, about 3 to about 7-fold, about 3 to about 8-fold, about 3 to about 9-fold, about 4 to about 7-fold, about 4 to about 8-fold, about 4 to about 9-fold, at least about 1.1-fold, at least about 1.5-fold, at least about 2-fold, at least about 2.5-fold, at least about 3-fold, at least about 3.5-fold, at least about 4-fold, at least about 5-fold, or at least about 10-fold. The control compound can be, for example, an oligonucleotide that is not complementary to the targeted portion of the pre-mRNA.

[0070]

[0156] Additionally, ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, and CD KL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHD DS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCN Q2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN. PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SC N3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPOR S, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH 14. MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1 Cells contacted with an ASO complementary to a targeted portion of the H4, STK11, PPARA, CYP2J2, or SYNGAP1 mRNA precursor transcript express the mature mRNA encoding the target protein, including: ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA , PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1. In some embodiments, the inhibitors of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OP A1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTA N1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1,mRNA encoding GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein, or ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, The amount of mature mRNA encoding SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein is increased by at least 10, 20, 30, 40, 50, 60, 80, 100, 150, 200, 250, 300, 350, 400, 450, 500, or 1000% compared to the amount of protein produced by the cell in the absence / absence of ASO treatment. In some embodiments, ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN 3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, K MT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF3 1, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2,UBE3A、V、 mRNA encoding CAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 proteins, or ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, CO produced in cells contacted with antisense oligomers L4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA 1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UB The total amount of mature mRNA encoding an E3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein is about 20% to about 300%, about 50% to about 300%, about 100% to about 300%, about 25% to about 300%, about 35% to about 350%, about 40% to about 400%, about 50% to about 500%, about 60% to about 600%, about 70% to about 700%, about 80% to about 800%, about 90% to about 900%, about 100% to about 1000%, about 110% to about 1100%, about 120% to about 1200%, about 130% to about 1300%, about 140% to about 1400%, about 150% to about 1500%, about 160% to about 1600%, about 170% to about 1700%, about 180% to about 1800%, about 190% to about 1900%, about 20% to about 2000%, about 25% to about 2000%, about 26% to about 2600%, about 27% to about 2700%, about 28% to about 2800%, about 29% to about 3000%, about 30% to about 3000%, about 31% to about 3100%, about 32% to about 3200%, about 3 150% to about 300%, about 20% to about 50%, about 20% to about 100%, about 20% to about 150%, about 20% to about 200%, about 20% to about 250%, about 50% to about 100%, about 50% to about 150%, about 50% to about 200%, about 50% to about 250%, about 100% to about 150%, about 100% to about 200%, about 100% to about 250%, about 150% to about 200%, about 150% to about 250%, about 200 to about 250%, at least about 10%, at least about 20%, at least about 50%, at least about 100%, at least about 150%,In some embodiments, the expression levels of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, P Encoding RPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 proteins ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, and NF-kappa-like domains are produced in cells contacted with mRNA or antisense oligomers. , PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE 3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2,Or, The total amount of mature mRNA encoding the SYNGAP1 protein is about 1.1 to about 10-fold, about 1.5 to about 10-fold, about 2 to about 10-fold, about 3 to about 10-fold, about 4 to about 10-fold, about 1.1 to about 5-fold, about 1.1 to about 6-fold, about 1.1 to about 7-fold, about 1.1 to about 8-fold, about 1.1 to about 9 ... An increase of about 5-fold, about 2 to about 6-fold, about 2 to about 7-fold, about 2 to about 8-fold, about 2 to about 9-fold, about 3 to about 6-fold, about 3 to about 7-fold, about 3 to about 8-fold, about 3 to about 9-fold, about 4 to about 7-fold, about 4 to about 8-fold, about 4 to about 9-fold, at least about 1.1-fold, at least about 1.5-fold, at least about 2-fold, at least about 2.5-fold, at least about 3-fold, at least about 3.5-fold, at least about 4-fold, at least about 5-fold, or at least about 10-fold. Control compounds include, for example, ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, The oligonucleotide may be complementary to the targeting portion of the SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 NIE-containing pre-mRNA.

[0071]

[0157] An NIE can be any length. In some embodiments, an NIE comprises the complete sequence of an intron, in which case it can be referred to as intron retention. In some embodiments, an NIE can be a portion of an intron. In some embodiments, an NIE can be the 5'-end portion of an intron including a 5'-ss sequence. In some embodiments, an NIE can be the 3'-end portion of an intron including a 3'-ss sequence. In some embodiments, an NIE can be a portion within an intron without including a 5'-ss sequence. In some embodiments, an NIE can be a portion within an intron without including a 3'-ss sequence. In some embodiments, an NIE can be a portion within an intron without including either a 5'-ss sequence or a 3'-ss sequence. In some embodiments, the NIE can be 5 to 10 nucleotides in length, 10 to 15 nucleotides in length, 15 to 20 nucleotides in length, 20 to 25 nucleotides in length, 25 to 30 nucleotides in length, 30 to 35 nucleotides in length, 35 to 40 nucleotides in length, 40 to 45 nucleotides in length, 45 to 50 nucleotides in length, 50 to 55 nucleotides in length, 55 to 60 nucleotides in length, 60 to 65 nucleotides in length, 65 to 70 nucleotides in length, 70 to 75 nucleotides in length, 75 to 80 nucleotides in length, 80 to 85 nucleotides in length, 85 to 90 nucleotides in length, 90 to 95 nucleotides in length, or 95 to 100 nucleotides in length. In some embodiments, the NIE is at least 10 nucleotides, at least 20 nucleotides, at least 30 nucleotides, at least 40 nucleotides, at least 50 nucleotides, at least 60 nucleoids, at least 70 nucleotides, at least 80 nucleotides in length, at least 90 nucleotides, or at least 100 nucleotides in length. In some embodiments, the NIE may be 100 to 200 nucleotides in length, 200 to 300 nucleotides in length, 300 to 400 nucleotides in length, 400 to 500 nucleotides in length, 500 to 600 nucleotides in length, 600 to 700 nucleotides in length, 700 to 800 nucleotides in length, 800 to 900 nucleotides in length, or 900 to 1000 nucleotides in length. In some embodiments, the NIE may be greater than 1000 nucleotides in length.

[0072]

[0158] The inclusion of a pseudoexon can result in a frameshift and the introduction of a premature termination codon (PIC) into the mature mRNA transcript, making the transcript a target for NMD. Mature mRNA transcripts containing an NIE can be non-productive mRNA transcripts that do not result in protein expression. The PIC can be located anywhere downstream of the NIE. In some embodiments, the PIC can be located in any exon downstream of the NIE. In some embodiments, the PIC can be located within the NIE. For example, ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPB exon 8x of ABCB4, exon 9x of ASS1, to mRNA transcripts encoded by L, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, or VCAN genes; ATP8B1 exon 16x, BAG3 exon 1x, CACNA1A exon 31x, CACNA1A exon 36x, CACNA1A exon 37x, CBS exon 3x, CBS exon 12x, CD55 exon 1x, CDKL5 exon 16x, CFH exon 3x, CHD2 exon 30x, CHRNA7 exon 4x, CISD2 exon 1x, CLN3 exon 15x, COL4A3 exon 11x of COL4A3, exon 41x of COL4A4, exon 22x of COL4A4, exon 44x of COL4A4, exon 20x of DEPDC5, exon 2x of DHDDS, exon 3x of ELOVL4, exon 5x of FAH, exon 4x of FXN, exon 4x of GALE, exon 3x of GBE1, exon 11x of GRIN2A, exon 1x of GRN, exon 2x of HEXA, exon 2x of KANSL1,KCNQ2 exon 1x, KMT2D exon 50x, MAPK3 exon 8x, MBD5 exon 13x, MECP2 exon 2x, MUT exon 11x, NF1 exon 31x, NIPBL exon 7x, NIPBL exon 38x, NSD1 exon 11x, OPA1 exon 6x, OPA1 exon 28x, OPTN exon 1x, PCCA exon 1x, PCCB exon 5x, PCCB exon 6x, PKP2 exon 4x, PLCB1 exon 23x, PRPF3 exon 3x, PRPF31 exon 9x, RAI1 exon 1x, RBFOX2 exon 5x, SCN2A exon 13x, SCN3A exon 6 Inclusion of exon 1x, SCN3A exon 7x, SCN8A exon 4x, SCN8A exon 6x, SCN8A exon 20x, SCN9A exon 6x, SHANK3 exon 24x, SLC25A13 exon 3x, SLC25A13 exon 6x, SLC25A13 exon 9x, SLC25A13 exon 11x, SLC25A13 exon 13x, SLC6A1 exon 1x, SPTAN1 exon 12x, TEK exon 10x, TEK exon 15x, TOPORS exon 1x, TSC2 exon 11x, TSC2 exon 30x, UBE3A exon 1x, or VCAN exon 7x can direct PIC into the mRNA transcript. For example, AKT3, CACNA1A, CBS, CD46, CFH, CHD2, CLN3, COL11A2, COL4A3, COL4A4, COL4A4, CR1, CRX, CYP2J2, DHDDS, DNAJC8, EIF2A, exons of AKT3 (GRCh38 / hg38:chr1 243564285 243564388); CACNA1A (GRCh38 / hg38:chr19 243564285 243564388); and CACNA1A (GRCh38 / hg38:chr19 243564285 243564388) to mRNA transcripts encoded by K3, ERN1, GALE, GUCY2F, GUCY2F, HEXA, HEXA, MAPK3, MBD5, MBD5, MBD5, MBD5, MUT, MYH14, MYO6, NF1, NF2, NIPBL, NR1H4, NSD1, NSD1, NSD1, NSD1, OPA1, OPA1, PCCA, PKP2, PPARA, PRPF3, PRPF3, SCN2A, SCN8A, SCN8A, SCN9A, SEMA3C, SEMA3D, SIRT3, STK11, STK11, SYNGAP1, TOPORS, or VCAN. exons of CBS (GRCh38 / hg38:chr21 43059730 43060012); exons of CD46 (GRCh38 / hg38:chr1 207775610 207775745); exons of CFH (GRCh38 / hg38:chr1 196675450 196675529); exons of CHD2 (GRCh38 / hg38:chr15 92998149 92998261); exons of CLN3 (GRCh38 / hg38:chr16 28479644 28479765); exons of COL11A2 (GRCh38 / hg38:chr6 COL4A3 exons (GRCh38 / hg38:chr2 227296487 227296526); COL4A4 exons (GRCh38 / hg38:chr2 227144653 227144833); COL4A4 exons (GRCh38 / hg38:chr2 227015283 227015360); CR1 exons (GRCh38 / hg38:chr1 207637688 207637848); CRX exons (GRCh38 / hg38:chr19 47835403 47835579); CYP2J2 exons (GRCh38 / hg38:chr1 59904366 59904516);DHDDS exon (GRCh38 / hg38:chr1 26442335 26442372);DNAJC8 exon (GRCh38 / hg38:chr1 28230131 28230252); EIF2AK3 exon (GRCh38 / hg38:chr2 88582755 88582824); ERN1 exon (GRCh38 / hg38:chr17 64102673 64102804); GALE exon (GRCh38 / hg38:chr1 23798311 23798484); GUCY2F exon (GRCh38 / hg38:chrX 109383365 109383446); GUCY2F exon (GRCh38 / hg38:chrX 109439038 109439175); HEXA exon (GRCh38 / hg38:chr15 72362376 72362466); HEXA exon (GRCh38 / hg38:chr15 72345677 72345776); MAPK3 exon (GRCh38 / hg38:chr16 30115595 30115645); MBD5 exon (GRCh38 / hg38:chr2 148460219 148460304); MBD5 exon (GRCh38 / hg38:chr2 148490695 148490787); MBD5 exon (GRCh38 / hg38:chr2 148505761 148505830; MUT exon (GRCh38 / hg38:chr6 49436522 49436597); MYH14 exon (GRCh38 / hg38:chr19 50230825 50230999); MYO6 exon (GRCh38 / hg38:chr6 75867431 75867523); NF1 exon (GRCh38 / hg38:chr17 31249955 31250125); NF2 exon (GRCh38 / hg38:chr22 29628658 29628773); NIPBL exon (GRCh38 / hg38:chr5 37048127 37048354); exon of NR1H4 (GRCh38 / hg38:chr12 100499841 100500024); exon of NSD1 (GRCh38 / hg38:chr5 177169394 177169559); exon of NSD1 (GRCh38 / hg38:chr5 177200761 177200783);exon of NSD1 (GRCh38 / hg38:chr5 1772; 47924 177248079); NSD1 exon (GRCh38 / hg38:chr5 177275947 177276101); OPA1 exon (GRCh38 / hg38:chr3 193628509 193628616); OPA1 exon (GRCh38 / hg38:chr3 193603500 193603557); PCCA exon (GRCh38 / hg38:chr13 100305751 100305834); PKP2 exon (GRCh38 / hg38:chr12 32894516 32894778); PPARA exon (GRCh38 / hg38:chr22 46203575 46203752); PRPF3 exon (GRCh38 / hg38:chr1 150327557 150327652); PRPF3 exon (GRCh38 / hg38:chr1 150330401 150330498); SCN2A exon (GRCh38 / hg38:chr2 165327155 165327202); exon of SCN8A (GRCh38 / hg38:chr12 exons of SCN8A (GRCh38 / hg38:chr12 51780202 51780271); exons of SCN9A (GRCh38 / hg38:chr2 166304238 166304329); exons of SEMA3C (GRCh38 / hg38:chr7 80794854 80794957); exons of SEMA3D (GRCh38 / hg38:chr7 85059498 85059541); exons of SIRT3 (GRCh38 / hg38:chr11 225673 226081); exons of STK11 (GRCh38 / hg38:chr19 1216268 1216398); exons of STK11 (GRCh38 / hg38:chr19 1221621 1221846); exons of SYNGAP1 (GRCh38 / hg38:chr6 33448789 33448868); exons of TOPORS (GRCh38 / hg38:chr9 32551365 32551469); exons of VCAN (GRCh38 / hg38:chr5 83544965 83545070) can direct PICs into mRNA transcripts. therapeutic agent

[0159] In various embodiments of the present disclosure, ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF4, PRPF5, PRPF6, PRPF7, PRPF8, PRPF9, PRPF10, PRPF11, PRPF12, PRPF13, PRPF14, PRPF15, PRPF16, PRPF17, PRPF18, PRPF19, PRPF20, PRPF21, PRPF22, PRPF23, PRPF24, PRPF25, PRPF26, PRPF27, PRPF28, PRPF29, PRPF30, PRPF31, PRPF32, PRPF41, PRPF52, PRPF53, PRPF54, PRPF55, PRPF6, PRPF75, PRPF8, PRPF96, PRPF19, PRPF16, PRPF18, PRPF19, PRPF21, PRPF22, PRPF23, PRPF24, PRPF35, PRPF19, PRPF25, PRPF36, PRPF19, PRPF25, PRPF37, PRPF19, PRPF26, PRPF28, PRPF38, PRPF41, PRPF55, PRPF56, PRPF57, PRPF58, PRPF59, PRPF61, PRPF72, PRPF Compositions and methods are provided that include therapeutic agents that modulate the protein expression levels of 1, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1. In some embodiments, ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, U BE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PP Compositions and methods for regulating alternative splicing of ARA, CYP2J2, or SYNGAP1 pre-mRNA are provided herein. In some embodiments, the following are present: ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, P LCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, C D46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1Induces exon skipping in pre-mRNA splicing, e.g., ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PC Provided herein are compositions and methods for inducing pseudoexon skipping during splicing of CA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 pre-mRNA. In other embodiments, therapeutic agents may be used to induce exon inclusion to reduce protein expression levels.

[0073]

[0160] The therapeutic agent disclosed herein can be an NIE inhibitor. The therapeutic agent may comprise a polynucleic acid polymer. According to one aspect of the present disclosure, functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3 , MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN 2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, CO 1. A method for treating or preventing a condition or disease associated with a deficiency of an L11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein, comprising administering an NIE inhibitor to a subject to inhibit functional ABCB4, ASS1, ATP8B1 , BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, O Provided herein are methods comprising increasing the level of PA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein, wherein the agent binds to a region of a pre-mRNA transcript that reduces inclusion of an NIE in the mature transcript. For example, functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, CO L4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT 2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31 , RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, 1. A method for treating or preventing a condition associated with a defect in a UBE3A or VCAN protein, comprising administering to a subject an NIE inhibitor to inhibit functional ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A,The method comprises increasing the level of SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, or VCAN protein, wherein the agent increases the level of an NIE (e.g., exon 8x of ABCB4, exon 9x of ASS1, exon 16x of ATP8B1, exon 1x of BAG3, exon 31x of CACNA1A, exon 36x of CACNA1A, exon 37x of CACNA1A, exon 3x of CBS, exon 12x of CBS, exon 1x of CD55, exon 1x of CDK L5 exon 16x, CFH exon 3x, CHD2 exon 30x, CHRNA7 exon 4x, CISD2 exon 1x, CLN3 exon 15x, COL4A3 exon 11x, COL4A3 exon 41x, COL4A4 exon 22x, COL4A4 exon 44x, DEPDC5 exon 20x, DHDDS exon 2x, ELOVL4 exon 3x, FAH exon 5x, FXN exon 4x, GALE exon 4x, GBE1 exon 3x, GRIN2A exon 11x, GRN exon 1x, HEXA exon 2x, KANSL1 exon 2x, KCNQ2 exon 1x, KMT2D exon 50x, MAPK3 exon 8x, MBD5 exon 13x, MECP2 exon 2x, MUT exon 11x, NF1 exon 31x, NIPBL exon 7x, NIPBL exon 38x, NSD1 exon 11x, OPA1 exon 6x, OPA1 exon 28x, OPTN exon 1x, PCCA exon 1x, PCCB exon 5x, PCCB exon 6x, PKP2 exon 4x, PLCB1 exon exon 23x, PRPF3 exon 3x, PRPF31 exon 9x, RAI1 exon 1x, RBFOX2 exon 5x, SCN2A exon 13x, SCN3A exon 6x, SCN3A exon 7x, SCN8A exon 4x, SCN8A exon 6x, SCN8A exon 20x, SCN9A exon 6x, SHANK3 exon 24x, SLC25A13 exon 3x, SLC25A13 exon 6x, SLC25A13 exon 9x, SLC25A13 exon 11x, SLC25A13 exon 13x,SLC6A1, Provided herein are methods for binding to a region of an intron containing exon 1x, exon 1x of SPTAN1, exon 12x of TEK, exon 10x of TEK, exon 15x of TOPORS, exon 1x of TSC2, exon 11x of TSC2, exon 30x of UBE3A, or exon 7x of VCAN, or an NIE activation control sequence in the same intron. For example, functional AKT3, CACNA1A, CBS, CD46, CFH, CHD2, CLN3, COL11A2, COL4A3, COL4A4, COL4A4, CR1, CRX, CYP2J2, DHDDS, DNAJC8, EIF2AK3, ERN1, GALE, GUCY2F, GUCY2F, HEXA, HEXA, MAPK3, MBD5, MBD5, MBD5, MBD5, MUT, MYH14, MYO6, NF1, NF2, NIPBL, NR1 1. A method for treating or preventing a condition associated with a deficiency of H4, NSD1, NSD1, NSD1, NSD1, OPA1, OPA1, PCCA, PKP2, PPARA, PRPF3, PRPF3, SCN2A, SCN8A, SCN8A, SCN9A, SEMA3C, SEMA3D, SIRT3, STK11, STK11, SYNGAP1, TOPORS, or VCAN protein, comprising administering to a subject an NIE inhibitor to produce functional AKT3, CACN A1A, CBS, CD46, CFH, CHD2, CLN3, COL11A2, COL4A3, COL4A4, COL4A4, CR1, CRX, CYP2J2, DHDDS, DNAJC8, EIF2AK3, ERN1, GALE, GUCY2F, GUCY2F, HEXA, HEXA, MAPK3, MBD5, MBD5, MBD5, MUT, MYH14, MYO6, NF1, NF2, NIPBL, NR1H4, NSD1, NSD1, NSD 1, including increasing the level of NSD1, OPA1, OPA1, PCCA, PKP2, PPARA, PRPF3, PRPF3, SCN2A, SCN8A, SCN8A, SCN9A, SEMA3C, SEMA3D, SIRT3, STK11, STK11, SYNGAP1, TOPORS, or VCAN protein, wherein the agent is a nucleotide exon (e.g., exon 243564285 243564388) of a precursor-mRNA transcript.CACNA1A exons (GRCh38 / hg38:chr19 13236449 13236618); CBS exons (GRCh38 / hg38:chr21 43059730 43060012); CD46 exons (GRCh38 / hg38:chr1 207775610 207775745); CFH exons (GRCh38 / hg38:chr1 196675450 196675529); CHD2 exons (GRCh38 / hg38:chr15 92998149 92998261); CLN3 exons (GRCh38 / hg38:chr16; 28479644 28479765; exons of COL11A2 (GRCh38 / hg38:chr6 33183634 33183698); exons of COL4A3 (GRCh38 / hg38:chr2 227296487 227296526); exons of COL4A4 (GRCh38 / hg38:chr2 227144653 227144833); exons of COL4A4 (GRCh38 / hg38:chr2 227015283 227015360); exons of CR1 (GRCh38 / hg38:chr1 207637688 207637848); exons of CRX (GRCh38 / hg38:chr19 47835403 47835579); CYP2J2 exons (GRCh38 / hg38:chr1 59904366 59904516); DHDDS exons (GRCh38 / hg38:chr1 26442335 26442372); DNAJC8 exons (GRCh38 / hg38:chr1 28230131 28230252); EIF2AK3 exons (GRCh38 / hg38:chr2 88582755 88582824); ERN1 exons (GRCh38 / hg38:chr17 64102673 64102804); GALE exons (GRCh38 / hg38:chr1 23798311 23798484); GUCY2F exon (GRCh38 / hg38:chrX 109383365 109383446); GUCY2F exon (GRCh38 / hg38:chrX 109439038 109439175); HEXA exon (GRCh38 / hg38:chr15 72362376 72362466); HEXA exon (GRCh38 / hg38:chr15 72345677 72345776; MAPK3 exon (GRCh38 / hg38:chr16 30115595 30115645); MBD5 exon (GRCh38 / hg38:chr2 148460219 148460304); MBD5 exon (GRCh38 / hg38:chr2 148490695 148490787); MBD5 exon (GRCh38 / hg38:chr2 148505761 148505830); MUT exon (GRCh38 / hg38:chr6 49436522 49436597); exon of MYH14 (GRCh38 / hg38:chr19 50230825 50230999); exon of MYO6 (GRCh38 / hg38:chr6 75867431 75867523); exon of NF1 (GRCh38 / hg38:chr17 31249955 312 50125); exon of NF2 (GRCh38 / hg38:chr22 29628658 29628773); exon of NIPBL (GRCh38 / hg38:chr5 37048127 37048354); exons of NR1H4 (GRCh38 / hg38:chr12 100499841 100500024); exons of NSD1 (GRCh38 / hg38:chr5 177169394 177169559); exons of NSD1 (GRCh38 / hg38:chr5 177200761 177200783); exons of NSD1 (GRCh38 / hg38:chr5 177247924 177248079); exons of NSD1 (GRCh38 / hg38:chr5 177275947 177276101); OPA1 exon (GRCh38 / hg38:chr3 193628509 193628616); OPA1 exon (GRCh38 / hg38:chr3 193603500 193603557); PCCA exon (GRCh38 / hg38:chr13 100305751 100305834); PKP2 exon (GRCh38 / hg38:chr12 32894516 32894778); PPARA exon (GRCh38 / hg38:chr22 46203575 46203752); PRPF3 exon (GRCh38 / hg38:chr1 150327557 150327652); exons of PRPF3 (GRCh38 / hg38:chr1 150330401 150330498); exons of SCN2A (GRCh38 / hg38:chr2 165327155 165327202); exons of SCN8A (GRCh38 / hg38:chr12 51688758 51688849); exons of SCN8A (GRCh38 / hg38:chr12 51780202 51780271); exons of SCN9A (GRCh38 / hg38:chr2 166304238 166304329); SEMA3C exon (GRCh38 / hg38:chr7 80794854 80794957); SEMA3D exon (GRCh38 / hg38:chr7 85059498 85059541); SIRT3 exon (GRCh38 / hg38:chr11 225673 226081); STK11 exon (GRCh38 / hg38:chr19 1216268 1216398); STK11 exon (GRCh38 / hg38:chr19 1221621 1221846); SYNGAP1 exon (GRCh38 / hg38:chr6 33448789 33448868); TOPORS exon (GRCh38 / hg38:chr9 32551365 32551469); VCAN exon (GRCh38 / hg38:chr5 83544965 83545070)), or to a region of an intron containing an NIE activation control sequence in the same intron.

[0074]

[0161] When referring to reducing NIE inclusion in mature mRNA, the reduction may be complete, e.g., 100%, or partial. The reduction may be clinically significant. The reduction / correction may be compared to the level of NIE inclusion in a subject without treatment, or compared to the amount of NIE inclusion in a population of similar subjects. Reduction / Correction can be at least 10% less NIE inclusion compared to the average subject or pre-treatment subject. The reduction can be at least 20% less NIE inclusion compared to the average subject or pre-treatment subject. The reduction can be at least 40% less NIE inclusion compared to the average subject or pre-treatment subject. The reduction can be at least 50% less NIE inclusion compared to the average subject or pre-treatment subject. The reduction can be at least 60% less NIE inclusion compared to the average subject or pre-treatment subject. The reduction can be at least 80% less NIE inclusion compared to the average subject or pre-treatment subject. The reduction can be at least 90% less NIE inclusion compared to the average subject or pre-treatment subject.

[0075]

[0162] Active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE 1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFO When referring to increasing X2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein levels, the increase may be clinically significant.The increase is in the activity of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, These were compared with the levels of PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 proteins. Even in a similar population of subjects, activity of ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRP The amount of F3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein may be compared.The increase is at least 10% more active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, F compared to the average subject or pre-treatment subjects. XN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1 , OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A 13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein. The increase is at least 20% more active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, The protein may be a PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein.The increase is at least 40% more active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, The protein may be a PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein.The increase is at least 50% more active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, The protein may be a PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein. The increase is at least 80% more active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOV compared to the average subject or pre-treatment subjects. L4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD 1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SL The protein may be a C25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein. The increase is at least 100% more active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB compared to the average subject or pre-treatment subjects , PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein.The increase is at least 200% more active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB compared to the average subject or pre-treatment subjects , PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein. The increase is at least 500% more active ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL compared to the average subject or pre-treatment subjects. 4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, ME CP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, S The protein may be a CN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 protein.

[0076]

[0163] In embodiments where the NIE inhibitor comprises a polynucleic acid polymer, the polynucleic acid polymer can be about 50 nucleotides in length. The polynucleic acid polymer can be about 45 nucleotides in length. The polynucleic acid polymer can be about 40 nucleotides in length. The polynucleic acid polymer can be about 35 nucleotides in length. The polynucleic acid polymer can be about 30 nucleotides in length. The polynucleic acid polymer can be about 24 nucleotides in length. The polynucleic acid polymer can be about 25 nucleotides in length. The polynucleic acid polymer can be about 20 nucleotides in length. The polynucleic acid polymer can be about 19 nucleotides in length. The polynucleic acid polymer can be about 18 nucleotides in length. The polynucleic acid polymer can be about 17 nucleotides in length. The polynucleic acid polymer can be about 16 nucleotides in length. The polynucleic acid polymer can be about 15 nucleotides in length. The polynucleic acid polymer can be about 14 nucleotides in length. The polynucleic acid polymer can be about 13 nucleotides in length. The polynucleic acid polymer can be about 12 nucleotides in length. The polynucleic acid polymer can be about 11 nucleotides in length. The polynucleic acid polymer can be about 10 nucleotides in length. The polynucleic acid polymer can be between about 10 and about 50 nucleotides in length. The polynucleic acid polymer can be between about 10 and about 45 nucleotides in length. A polynucleic acid polymer can be between about 10 and about 40 nucleotides in length. A polynucleic acid polymer can be between about 10 and about 35 nucleotides in length. A polynucleic acid polymer can be between about 10 and about 30 nucleotides in length. A polynucleic acid polymer can be between about 10 and about 25 nucleotides in length. A polynucleic acid polymer can be between about 10 and about 20 nucleotides in length. A polynucleic acid polymer can be between about 15 and about 25 nucleotides in length. A polynucleic acid polymer can be between about 15 and about 30 nucleotides in length. A polynucleic acid polymer can be between about 12 and about 30 nucleotides in length.

[0077]

[0164] The sequence of the polynucleic acid polymer can be at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% complementary to the target sequence of an mRNA transcript, such as a partially processed mRNA transcript. The sequence of the polynucleic acid polymer can also be 100% complementary to the target sequence of a pre-mRNA transcript.

[0078]

[0165] The sequence of the polynucleic acid polymer may have four or fewer mismatches with the target sequence of the pre-mRNA transcript. The sequence of the polynucleic acid polymer may have three or fewer mismatches with the target sequence of the pre-mRNA transcript. The sequence of the polynucleic acid polymer may have two or fewer mismatches with the target sequence of the pre-mRNA transcript. The sequence of the polynucleic acid polymer may have one or fewer mismatches with the target sequence of the pre-mRNA transcript. The sequence of the polynucleic acid polymer may have no mismatches with the target sequence of the pre-mRNA transcript.

[0079]

[0166] Polynucleic acid polymer can be specifically hybridized with the target sequence of mRNA precursor transcript.For example, polynucleic acid polymer can have 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5% or 100% sequence complementarity with the target sequence of mRNA precursor transcript.Hybridization can be carried out under highly stringent hybridization conditions.

[0080]

[0167] The polynucleic acid polymer comprises a sequence having at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% sequence identity to a sequence selected from the group consisting of SEQ ID NOs: 60-191. The polynucleic acid polymer may comprise a sequence having 100% sequence identity to a sequence selected from the group consisting of SEQ ID NOs: 60-191.

[0081]

[0168] When referring to a polynucleic acid polymer sequence, one of skill in the art will recognize one or more substitutions It will be understood that up to 1000 substitutions may be tolerated, and optionally two substitutions may be tolerated in the sequence, such that the polynucleic acid polymer sequence maintains its ability to hybridize to, or, if the substitution is in, the target sequence, be recognized as the target sequence. The sequence identity criteria may be determined by BLAST sequence alignment using standard / default parameters. For example, a sequence may have 99% identity and still function according to the present disclosure. In other embodiments, a sequence may have 98% identity and still function according to the present disclosure. In another embodiment, a sequence may have 95% identity and still function according to the present disclosure. In another embodiment, a sequence may have 90% identity and still function according to the present disclosure. Antisense oligomers

[0169] ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN , GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, P Provided herein are compositions comprising an antisense oligomer that induces exon skipping by binding to a targeted portion of an RPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 NIE-containing pre-mRNA.As used herein, the terms "ASO" and "antisense oligomer" are used interchangeably and refer to an ASO that binds to a target nucleic acid (e.g., ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, N " refers to an oligomer such as a polynucleotide containing nucleobases that hybridize to a sequence of an NIE-containing precursor-mRNA (e.g., F1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 NIE-containing precursor-mRNA). ASOs can have exact sequence complementarity to a target sequence or very high complementarity (e.g., sufficient complementarity to bind the target sequence and enhance splicing at the splice site). ASOs are designed to bind (hybridize) to a target nucleic acid (e.g., the targeting portion of a pre-mRNA transcript) and remain hybridized under physiological conditions. Typically, when an ASO hybridizes to a site other than the intended (targeting) nucleic acid sequence, it hybridizes to a limited number of sequences that are not the target nucleic acid (a small number of sites other than the target nucleic acid). ASO design may take into account the presence of the nucleic acid sequence in the targeting portion of the pre-mRNA transcript or the presence of sufficiently similar nucleic acid sequences elsewhere in the genome or pre-mRNA or transcriptome of a cell, so as to limit the possibility that the ASO will bind to other sites and cause "off-target" effects.As known in the art, for example, "Reduce." Any of the antisense oligomers in PCT Application No. PCT / US2014 / 054151, published as WO2015 / 035091, entitled "Inducing Nonsense-Mediated mRNA Decay," can be used to practice the methods described herein.

[0082]

[0170] In some embodiments, the ASO "specifically hybridizes" or is "specific" for the targeted portion of the target nucleic acid or NIE-containing pre-mRNA. Typically, such hybridization occurs at a T substantially above 37°C, preferably at least 50°C, and typically between 60°C and approximately 90°C. m Such hybridization preferably corresponds to stringent hybridization conditions. For a given ionic strength and pH, T m is the temperature at which 50% of the target sequence hybridizes to a complementary oligonucleotide.

[0083]

[0171] Oligomers, such as oligonucleotides, are " complementary " to each other when hybridization occurs between two single-stranded polynucleotides in antiparallel configuration.A double-stranded polynucleotide can be " complementary " to another polynucleotide when hybridization can occur between one of the strands of a first polynucleotide and a second polynucleotide.Complementarity (the degree to which one polynucleotide is complementary to another polynucleotide) can be quantified in terms of the proportion (e.g., percentage) of bases that are expected to form hydrogen bonds with each other in opposite strands according to generally accepted base pairing rules.The sequence of antisense oligomer (ASO) does not need to be 100% complementary to the sequence of the target nucleic acid that hybridizes. In certain embodiments, an ASO may contain at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence complementarity to a target region within a target nucleic acid sequence. For example, an ASO in which 18 of 20 nucleobases of an oligomeric compound are complementary to a target region and thus capable of specifically hybridizing would represent 90 percent complementarity. In this example, the remaining non-complementary nucleobases may be clustered together or interspersed with complementary nucleobases, and need not be contiguous to each other or to complementary nucleobases. The percent complementarity of an ASO with a region of a target nucleic acid can be routinely determined using the BLAST (basic local alignment search tool) and PowerBLAST programs known in the art (Altschul et al., J. Mol. Biol., 1990, 215, 403-410; Zhang and Madden, Genome Res., 1997, 7, 649-656).

[0084]

[0172] ASO does not need to hybridize to all nucleobases in the target sequence, and the nucleobases that ASO hybridizes can be contiguous or discontinuous.ASO may hybridize across one or more segments of a pre-mRNA transcript, such that intervening or adjacent segments are not involved in the hybridization event (e.g., a loop structure or a hairpin structure may be formed).In certain embodiments, ASO hybridizes to non-contiguous nucleobases in the target pre-mRNA transcript.For example, ASO can hybridize to nucleobases in a pre-mRNA transcript that are separated by one or more nucleobases that ASO does not hybridize to.

[0085]

[0173] The ASOs described herein contain nucleobases that are complementary to nucleobases present in the target portion of the NIE-containing pre-mRNA. The term ASO includes oligonucleotides and any other oligomeric molecules that contain nucleobases that can hybridize to complementary nucleobases in the target mRNA but do not contain sugar moieties, such as peptide nucleic acids (PNAs). ASOs can be composed of naturally occurring nucleotides, nucleotide analogs, modified nucleotides, or any other oligomeric molecule that contains nucleobases that can hybridize to complementary nucleobases in the target mRNA. The term "naturally occurring nucleotide" includes deoxyribonucleotides and ribonucleotides. The term "modified nucleotide" includes nucleotides with modified or substituted sugar groups and / or modified backbones. In some embodiments, all nucleotides in the ASO are modified nucleotides. Chemical modifications of ASOs or components of ASOs that are compatible with the methods and compositions described herein will be apparent to those skilled in the art and can be found, for example, in U.S. Patent No. 8,258,109 B2, U.S. Patent No. 5,656,612, U.S. Patent Publication No. 2012 / 0190728, and Dias and Stein, Mol. Cancer Ther. 2002, 347-355, which are incorporated herein by reference in their entirety.

[0086]

[0174] The nucleobase(s) of the ASO may be any naturally occurring unmodified nucleobase, such as adenine, guanine, cytosine, thymine, and uracil, or any synthetic or modified nucleobase sufficiently similar to an unmodified nucleobase to be capable of hydrogen bonding with a nucleobase present in the target pre-mRNA. Examples of modified nucleobases include, but are not limited to, hypoxanthine, xanthine, 7-methylguanine, 5,6-dihydrouracil, 5-methylcytosine, and 5-hydroxymethylcytosine.

[0087]

[0175] The ASOs described herein also include backbone structures that connect the components of the oligomer. The terms "backbone structure" and "oligomeric linkage" can be used interchangeably and refer to the connections between the monomers of the ASO. In naturally occurring oligonucleotides, the backbone includes 3'-5' phosphodiester linkages that connect the sugar moieties of the oligomer. The backbone structures or oligomeric linkages of the ASOs described herein include (but are not limited to) phosphorothioate, phosphorodithioate, phosphoroselenoate, phosphorodiselenoate, phosphoroanilothioate, phosphoroaniladate, and phosphoroamidate. See, for example, LaPlanche et al., Nucleic Acids Res. 14:9081 (1986); Stec et al., J. Am. Chem. Soc. 106:6077 (1984); Stein et al., Nucleic Acids Res. 16:3209 (1988); Zon et al., Anti-Cancer Drug Design 6:539 (1991); Zon et al., Oligonucleotides and Analogues: A Practical Approach, pp. 87-108 (F. Eckstein, ed., Oxford University Press, Oxford, England (1991)); Stec et al., U.S. Pat. No. 5,151,510; Uhlmann and Peyman, Chemical Reviews 90:543 (1990). In some embodiments, the backbone structure of the ASO does not contain phosphorus, but rather peptide bonds, e.g., peptide nucleic acids (PNAs), or linking groups including carbamates, amides, and linear and cyclic hydrocarbon groups. In some embodiments, the backbone modification is a phosphothioate linkage. In some embodiments, the backbone modification is a phosphoramidate linkage.

[0088]

[0176] In some embodiments, the stereochemistry at each phosphorus internucleotide linkage of the ASO backbone is disordered. In some embodiments, the stereochemistry at each phosphorus internucleotide linkage of the ASO backbone is controlled, not disordered. For example, U.S. Patent Application Publication No. 2014 / 0194610, "Methods for the Synthesis of Functionalized Nucleic Acids," incorporated herein by reference, describes methods for independently selecting the handedness of chirality at each phosphorus atom in a nucleic acid oligomer. In some embodiments, ASOs used in the methods of the disclosure, including but not limited to any ASOs listed in Tables 5 and 6 herein, are ASOs with non-disordered phosphorus internucleotide linkages. In some embodiments, the compositions used in the methods of the present disclosure comprise a diastereomeric pure ASO. In some embodiments, the compositions used in the methods of the present disclosure comprise an ASO with a diastereomeric purity of at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, about 100%, about 90% to about 100%, about 91% to about 100%, about 92% to about 100%, about 93% to about 100%, about 94% to about 100%, about 95% to about 100%, about 96% to about 100%, about 97% to about 100%, about 98% to about 100%, or about 99% to about 100%.

[0089]

[0177] In some embodiments, the ASO has a non-random mixture of Rp and Sp configurations at the phospho-internucleotide linkages. For example, it has been suggested that a mixture of Rp and Sp is required to achieve a balance between good activity and nuclease stability in antisense oligonucleotides (Wan et al., 2014, "Synthesis, biophysical properties and biological activity of second generation antisense oligonucleotides," incorporated herein by reference). "containing chiral phosphorothioate linkages", Nucleic Acids Research 42(22):13456~13468). In some embodiments, the ASOs used in the methods of the disclosure, including but not limited to, any of the ASOs set forth herein in SEQ ID NOS: 60-191, comprise about 5-100% Rp, at least about 5% Rp, at least about 10% Rp, at least about 15% Rp, at least about 20% Rp, at least about 25% Rp, at least about 30% Rp, at least about 35% Rp, at least about 40% Rp, at least about 45% Rp, at least about 50% Rp, at least about 55% Rp, at least about 60% Rp, at least about 65% Rp, at least about 70% Rp, at least about 75% Rp, at least about 80% Rp, at least about 85% Rp, at least about 90% Rp, or at least about 95% Rp with the remainder being Sp, or about 100% Rp. In some embodiments, the ASOs used in the methods of the disclosure, including but not limited to any ASO described herein, comprising a sequence having at least about 80%, 85%, 90%, 95%, 97%, or 100% sequence identity to a region comprising at least 8 consecutive nucleic acids of any one of SEQ ID NOs: 60-191, can be from about 10% to about 100% Rp, from about 15% to about 100% Rp, from about 20% to about 100% Rp, from about 25% to about 100% Rp, from about 30% to about 100% Rp, from about 35% to about 100% Rp, from about 40% to about 100% Rp, from about 45% to about 100% Rp, from about 50% to about 100% Rp, from about 55% to about 100% Rp, from about 60% to about 100% Rp, from about 65% to about 100% Rp, from about 70% to about 100% Rp, from about 75% to about 100% Rp, from about 80% to about 100% Rp, from about 85% to about 100% Rp, from about 85% to about 100% Rp, from about 90% to about 100% Rp, from about 95% to about 100% Rp, from about 95% to about 100% Rp, from about 10 ... Rp, about 45% to about 100% Rp, about 50% to about 100% Rp, about 55% to about 100% Rp, about 60% to about 100% Rp, about 65% to about 100% Rp, about 70% to about 100% Rp, about 75% to about 100% Rp, about 80% to about 100% Rp, about 85% to about 100% Rp, about 90% to about 100% Rp, or about 95% to about 100% Rp, about 20% to about 80% Rp, about 25% to about 75% Rp, about 30% to about 70% Rp, about 40% to about 60% Rp, or about 45% to about 55% Rp and the remainder Sp.

[0090]

[0178] In some embodiments, the ASOs used in the methods of the disclosure, including but not limited to any ASO described herein, comprising a sequence having at least about 80%, 85%, 90%, 95%, 97%, or 100% sequence identity to a region comprising at least 8 consecutive nucleic acids of any one of SEQ ID NOs: 60-191, can be about 5-100% Sp, at least about 5% Sp, at least about 10% Sp, at least about 15% Sp, at least about 20% Sp, at least about 25% Sp, at least about 30% Sp, at least about 35% Sp, at least about 40% Sp, at least about 45% Sp, at least about 50% Sp, at least about 55% Sp, at least about 60% Sp, at least about 65 ... It contains 5% Sp, at least about 50% Sp, at least about 55% Sp, at least about 60% Sp, at least about 65% Sp, at least about 70% Sp, at least about 75% Sp, at least about 80% Sp, at least about 85% Sp, at least about 90% Sp, or at least about 95% Sp with the remainder Rp, or about 100% Sp. In embodiments, the ASOs used in the methods of the disclosure, including but not limited to any ASO described herein, comprising a sequence having at least about 80%, 85%, 90%, 95%, 97%, or 100% sequence identity to a region comprising at least 8 consecutive nucleic acids of any one of SEQ ID NOs: 60-191, can be from about 10% to about 100% Sp, from about 15% to about 100% Sp, from about 20% to about 100% Sp, from about 25% to about 100% Sp, from about 30% to about 100% Sp, from about 35% to about 100% Sp, from about 40% to about 100% Sp, from about 45% to about 100% Sp, from about 50% to about 100% Sp, from about 55% to about 100% Sp, from about 60% to about 100% Sp, from about 65% to about 100% Sp, from about 70% to about 100% Sp, from about 75% to about 100% Sp, from about 80% to about 100% Sp, from about 85% to about 100% Sp, from about 85% to about 100% Sp, from about 90% to about 100% Sp, from about 95% to about 100% Sp, from about 95% to about 100% Sp, from about 10 ... Sp, about 45% to about 100% Sp, about 50% to about 100% Sp, about 55% to about 100% Sp, about 60% to about 100% Sp, about 65% to about 100% Sp, about 70% to about 100% Sp, about 75% to about 100% Sp, about 80% to about 100% Sp, about 85% to about 100% Sp, about 90% to about 100% Sp, or about 95% to about 100% Sp, about 20% to about 80% Sp, about 25% to about 75% Sp, about 30% to about 70% Sp, about 40% to about 60% Sp, or about 45% to about 55% Sp, with the remainder being Rp.

[0091]

[0179] Any ASO described herein may contain a sugar moiety containing ribose or deoxyribose, as found in naturally occurring nucleotides, or a modified sugar moiety or sugar analog, such as a morpholine ring. Non-limiting examples of modified sugar moieties include 2'-substituents such as 2'-O-methyl (2'-O-Me), 2'-O-methoxyethyl (2'MOE), 2'-O-aminoethyl, 2'F;N3'→P5' phosphoramidate, 2'dimethylaminooxyethoxy, 2'dimethylaminoethoxyethoxy, 2'-guanidinium, 2'-O-guanidinium ethyl, carbamate-modified sugars, and bicyclic-modified sugars. In some embodiments, the sugar moiety modification is selected from 2'-O-Me, 2'F, and 2'MOE. In some embodiments, the sugar moiety modification is an additional crosslink, such as in locked nucleic acids (LNAs). In some embodiments, the sugar analog contains a morpholine ring, e.g., phosphorodiamidate morpholino (PMO). In some embodiments, the sugar moiety comprises a ribofuransyl or 2'deoxyribofuransyl modification. In some embodiments, the sugar moiety comprises a 2'4'-constrained 2'O-methyloxyethyl (cMOE) modification. In some embodiments, the sugar moiety comprises a cEt 2',4'-constrained 2'-O-ethyl BNA modification. In some embodiments, the sugar moiety comprises a tricycloDNA (tcDNA) modification. In some embodiments, the sugar moiety comprises an ethylene nucleic acid (ENA) modification. In some embodiments, the sugar moiety comprises an MCE modification. Modifications are known in the art and are described, for example, in Jarver et al., 2014, "A Chemical View of Oligonucleotides for Exon Skipping and Related Drug Applications," Nucleic Acid Therapeutics 24(1):37-47, which is incorporated herein by reference for this purpose.

[0092]

[0180] In some embodiments, each monomer of an ASO is modified in the same way, for example, each linkage in the backbone of the ASO contains a phosphorothioate linkage, or each ribose sugar moiety contains a 2'O-methyl modification. Such modifications present in each of the monomer components of an ASO are referred to as "uniform modifications." In some cases, a combination of different modifications may be desired; for example, an ASO may contain a combination of phosphorodiamidate linkages and sugar moieties containing morpholine rings (morpholinos). A combination of different modifications to an ASO is referred to as a "mixed modification" or "mixed chemistry."

[0093]

[0181] In some embodiments, the ASO comprises one or more backbone modifications. In some embodiments, the ASO comprises one or more sugar moiety modifications. In some embodiments, the ASO comprises one or more backbone modifications and one or more sugar moiety modifications. In some embodiments, the ASO comprises a 2'MOE modification and a phosphorothioate backbone. In some embodiments, the ASO comprises a phosphorodiamidate morpholino (PMO). In some embodiments, the ASO comprises a peptide nucleic acid (PNA). Any ASO described herein or any component of the ASO (e.g., nucleobase, sugar moiety, backbone) may be modified to achieve a desired property or activity of the ASO or to reduce an undesired property or activity of the ASO. For example, the ASO, or one or more components of any ASO, may be modified to increase binding affinity for the target sequence of a pre-mRNA transcript, to decrease binding to any non-target sequences, to decrease degradation by cellular nucleases (i.e., RNase H), to improve uptake of the ASO into the cell and / or cell nucleus, to alter the pharmacokinetics or pharmacodynamics of the ASO, and / or to modulate the half-life of the ASO.

[0094]

[0182] In some embodiments, ASOs are composed of 2'-O-(2-methoxyethyl) (MOE) phosphorothioate-modified nucleotides. ASOs composed of such nucleotides are particularly well suited for the methods disclosed herein, as oligomers with such modifications have been shown to have significantly enhanced resistance to nuclease degradation and increased bioavailability, making them suitable for oral delivery, for example, in some embodiments described herein. See, e.g., Geary et al., J Pharmacol Exp Ther. 2001; 296(3):890-7; Geary et al., J Pharmacol Exp Ther. 2001; 296(3):898-904.

[0095]

[0183] Methods for synthesizing ASOs will be known to those of skill in the art. Alternatively, or additionally, ASOs may be obtained from commercial suppliers.

[0184] Unless otherwise specified, the left-hand end of a single-stranded nucleic acid (e.g., a pre-mRNA transcript, an oligonucleotide, an ASO, etc.) sequence is the 5' end, and the left-hand direction of a single-stranded or double-stranded nucleic acid sequence is referred to as the 5' direction. Similarly, the right-hand end or direction of a nucleic acid sequence (single-stranded or double-stranded) is the 3' end or direction. Generally, a region or sequence 5' to a reference point in a nucleic acid is referred to as "upstream," and a region or sequence 3' to a reference point in a nucleic acid is referred to as "downstream." Generally, the 5' direction or end of an mRNA is where the initiation or start codon is located, and the 3' end or direction is where the stop codon is located. In some embodiments, nucleotides upstream of the reference point in a nucleic acid may be designated by a negative number, and nucleotides downstream of the reference point may be designated by a positive number. For example, a reference point (e.g., an exon-exon junction in an mRNA) may be designated as the "zero" site, the nucleotide immediately adjacent to the reference point upstream is designated as "minus one," e.g., "-1," and the nucleotide immediately adjacent to the reference point downstream is designated as "plus one," e.g., "+1."

[0096]

[0185] Additionally, ASO includes ABCB4, ASS1, ATP8B1, BAG3, and CACN A1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3 COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D APK3, MBD5, MECP2, MUT, NF1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX 2. SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3 D46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, PPARA, CYP2J2, or SYNGAP1 The following genes are located downstream (3' direction) of the 5' splice site of the included exon (or the 3' end of the NIE) in the NIE-containing pre-mRNA (e.g., the direction indicated by a positive number relative to the 5' splice site): ABCB4, ASS1, ATP8B1, BAG3, CACNA1A, CBS, CD55, CDKL5, CFH, CHD2, CHRNA7, CISD2, CLN3, COL4A3, COL4A4, DEPDC5, DHDDS, ELOVL4, FAH, FXN, GALE, GBE1, GRIN2A, GRN, HEXA, KANSL1, KCNQ2, KMT2D, MAPK3, MBD5, MECP2, MUT, N is complementary to (and binds to) a targeting portion of an F1, NIPBL, NSD1, OPA1, OPTN, PCCA, PCCB, PKP2, PLCB1, PRPF3, PRPF31, RAI1, RBFOX2, SCN2A, SCN3A, SCN8A, SCN9A, SHANK3, SLC25A13, SLC6A1, SPTAN1, TEK, TOPORS, TSC2, UBE3A, VCAN, AKT3, CD46, COL11A2, CR1, CRX, DNAJC8, MYH14, MYO6, NF2, SEMA3C, SEMA3D, EIF2AK3, ERN1, GUCY2F, SIRT3, NR1H4, STK11, P...

Claims

1. A pharmaceutical composition comprising an antisense oligomer and a pharmaceutically acceptable excipient, the antisense oligomer binds to a targeted portion of a pre-mRNA that contains a nonsense-mediated mRNA decay-inducing exon (NMD exon) and encodes a target protein; the antisense oligomer promotes exclusion of the NMD exon from the pre-mRNA, thereby increasing the level of processed mRNA encoding the target protein and increasing expression of the target protein in cells containing the pre-mRNA; the target protein is SYNGAP1, The NMD exon is identified by the pair of genomic coordinates GRCh38 / hg38:chr6 33448789 33448868, and The targeting portion of the pre-mRNA (a) at least partially overlaps with an NMD exon identified by a pair of genomic coordinates; or (b) up to 20 nucleotides upstream (or in the 5' direction) from GRCh38 / hg38:chr6 33448789 or up to 20 nucleotides downstream (or in the 3' direction) from GRCh38 / hg38:chr6 33448868; The pharmaceutical composition.

2. The pharmaceutical composition of claim 1, wherein the exclusion of the NMD exon from the pre-mRNA encoding the target protein in cells contacted with the antisense oligomer is increased by at least 1.1-fold compared to the exclusion of the NMD exon from the processed mRNA encoding the target protein in control cells not contacted with the antisense oligomer.

3. 3. The pharmaceutical composition of claim 1, wherein the level of processed mRNA encoding the target protein produced in cells contacted with the antisense oligomer is increased by at least 1.1-fold compared to the level of processed mRNA encoding the target protein in control cells not contacted with the antisense oligomer.

4. 4. The pharmaceutical composition of claim 1, wherein the level of the target protein produced in cells contacted with the antisense oligomer is increased by at least 1.1-fold compared to the level of the target protein produced in control cells not contacted with the antisense oligomer.

5. 5. The pharmaceutical composition of any one of claims 1 to 4, wherein the pre-mRNA encoding the target protein is encoded by a gene sequence having at least 90%, 95%, 97%, or 100% sequence identity to SEQ ID NO:

211.

6. A pharmaceutical composition described in any one of claims 1 to 5, wherein the targeting moiety is located in an intron region between two standard exon regions of a pre-mRNA encoding the target protein, the intron region containing an NMD exon defined by a pair of genomic coordinates, and the targeting moiety comprises a sequence having at least 90%, 95%, 97%, or 100% sequence identity to SEQ ID NO:

189.

7. 7. The pharmaceutical composition of claim 6, wherein the antisense oligomer is 12 to 50 nucleobases in length, is an antisense oligomer (ASO), and comprises a sequence that is at least 90%, 95%, 97%, or 100% complementary to a targeted portion of the pre-mRNA.

8. The pharmaceutical composition of any one of claims 1 to 7, wherein the targeting portion at least partially overlaps with an NMD exon identified by a pair of genomic coordinates.

9. 8. The pharmaceutical composition of any one of claims 1 to 7, wherein the targeting moiety is up to 20 nucleotides upstream (or in the 5' direction) from GRCh38 / hg38:chr6 33448789 or up to 20 nucleotides downstream (or in the 3' direction) from GRCh38 / hg38:chr6 33448868.

10. The pharmaceutical composition of any one of claims 1 to 7, wherein the targeting moiety comprises an exon-intron junction of an NMD exon specified by a pair of genomic coordinates.

11. The pharmaceutical composition of any one of claims 1 to 7, wherein the targeting moiety is within an NMD exon specified by a pair of genomic coordinates.

12. The pharmaceutical composition of any one of claims 1 to 7, wherein the targeting moiety comprises 12 or more contiguous nucleotides of an NMD exon specified by a pair of genomic coordinates.

13. The pharmaceutical composition according to any one of claims 1 to 12, wherein the target protein produced is a full-length protein or a wild-type protein.

14. 14. The pharmaceutical composition of any one of claims 1 to 13, wherein the antisense oligomer comprises a backbone modification comprising a phosphorothioate or phosphorodiamidate linkage.

15. 14. The pharmaceutical composition of any one of claims 1 to 13, wherein the antisense oligomer comprises a phosphorodiamidate morpholino, locked nucleic acid, peptide nucleic acid, 2'-O-methyl, 2'-fluoro, or 2'-O-methoxyethyl moiety.

16. The pharmaceutical composition of any one of claims 1 to 13, wherein the antisense oligomer comprises at least one modified sugar moiety.

17. 17. The pharmaceutical composition of claim 16, wherein each sugar moiety is a modified sugar moiety.

18. 14. The pharmaceutical composition of any one of claims 1 to 13, wherein the antisense oligomer is 12 to 20 nucleobases in length.

19. A pharmaceutical composition according to any one of claims 1 to 18 for use in treating a disease or condition in a subject in need thereof.

20. 20. The pharmaceutical composition of claim 19, wherein the disease or condition is associated with deficient amounts or activity of the target protein.

21. 20. The pharmaceutical composition of claim 19, wherein the disease or condition is associated with a loss-of-function mutation in the target protein.

22. 20. The pharmaceutical composition of claim 19, wherein the disease or condition is associated with haploinsufficiency of a gene encoding the target protein, and the subject has a first allele that encodes a functional target protein and a second allele in which the target protein is not produced or is produced at a reduced level, or a second allele that encodes a non-functional or partially functional target protein.

23. The disease or condition is associated with an autosomal dominant mutation in a gene encoding a target protein, and the subject: (i) the target protein is not produced or is produced at a reduced level compared to the wild-type allele, or (ii) the target protein produced is non-functional or partially functional compared to the wild-type allele have a first allele, and (iii) the target protein is produced at a reduced level compared to the wild-type allele, and the target protein produced is at least partially functional compared to the wild-type allele; or (iv) the target protein produced is partially functional compared to the wild-type allele 20. The pharmaceutical composition of claim 19, having a second allele.

24. 20. The pharmaceutical composition of claim 19, wherein the disease or condition comprises autosomal dominant mental retardation 5.

25. The composition according to any one of claims 19 to 24, wherein the subject is a human.

26. 26. The pharmaceutical composition of any one of claims 19 to 25, wherein the antisense oligomer is administered to a subject by intrathecal, intracerebroventricular, intraperitoneal, intramuscular, subcutaneous, intravitreal, or intravenous injection.

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