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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for USH1C |
 Gene summary |
| Gene information | Gene symbol | USH1C | Gene ID | 10083 |
| Gene name | USH1 protein network component harmonin | |
| Synonyms | AIE-75|DFNB18|DFNB18A|NY-CO-37|NY-CO-38|PDZ-45|PDZ-73|PDZ-73/NY-CO-38|PDZ73|PDZD7C|ush1cpst | |
| Cytomap | 11p15.1 | |
| Type of gene | protein-coding | |
| Description | harmoninUsher syndrome 1C (autosomal recessive, severe)antigen NY-CO-38/NY-CO-37autoimmune enteropathy-related antigen AIE-75renal carcinoma antigen NY-REN-3usher syndrome type-1C protein | |
| Modification date | 20180526 | |
| UniProtAcc | Q9Y6N9 | |
| Context | PubMed: USH1C [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| USH1C | GO:0034622 | cellular protein-containing complex assembly | 26812018 |
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Exon skipping events across known transcript of Ensembl for USH1C from UCSC genome browser |
| Skipped exons in TCGA and GTEx based on Ensembl gene isoform structure. * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Gene isoform structures and expression levels for USH1C |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for USH1C |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_69594 | 11 | 17515878:17515923:17517115:17517224:17518304:17518360 | 17517115:17517224 | ENSG00000006611.11 | ENST00000005226.7 |
| exon_skip_69598 | 11 | 17515878:17515923:17518304:17518360:17519708:17519818 | 17518304:17518360 | ENSG00000006611.11 | ENST00000318024.4,ENST00000529563.1,ENST00000526313.1,ENST00000527720.1,ENST00000527020.1 |
| exon_skip_69610 | 11 | 17518304:17518360:17519708:17519818:17522597:17522694 | 17519708:17519818 | ENSG00000006611.11 | ENST00000318024.4,ENST00000529563.1,ENST00000526313.1,ENST00000527720.1,ENST00000005226.7,ENST00000527020.1 |
| exon_skip_69637 | 11 | 17523485:17523527:17538947:17539021:17542416:17542509 | 17538947:17539021 | ENSG00000006611.11 | ENST00000318024.4,ENST00000527720.1,ENST00000527020.1 |
| exon_skip_69658 | 11 | 17533448:17533601:17537787:17537837:17542416:17542509 | 17537787:17537837 | ENSG00000006611.11 | ENST00000005226.7 |
| exon_skip_69662 | 11 | 17535987:17536173:17537787:17537837:17538947:17539021 | 17537787:17537837 | ENSG00000006611.11 | ENST00000530700.1 |
| exon_skip_69663 | 11 | 17537787:17537837:17538947:17539021:17542416:17542509 | 17538947:17539021 | ENSG00000006611.11 | ENST00000530700.1 |
| exon_skip_69665 | 11 | 17544429:17544473:17544757:17544814:17544965:17545025 | 17544757:17544814 | ENSG00000006611.11 | ENST00000318024.4,ENST00000526181.1,ENST00000526313.1,ENST00000527720.1,ENST00000005226.7 |
| exon_skip_69666 | 11 | 17552700:17552839:17552945:17553089:17554801:17554869 | 17552945:17553089 | ENSG00000006611.11 | ENST00000318024.4,ENST00000526181.1,ENST00000526313.1,ENST00000527720.1,ENST00000005226.7,ENST00000527020.1 |
| exon_skip_69668 | 11 | 17552980:17553089:17554801:17554869:17565818:17565854 | 17554801:17554869 | ENSG00000006611.11 | ENST00000318024.4,ENST00000005226.7,ENST00000527020.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for USH1C |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_69594 | 11 | 17515878:17515923:17517115:17517224:17518304:17518360 | 17517115:17517224 | ENSG00000006611.11 | ENST00000005226.7 |
| exon_skip_69598 | 11 | 17515878:17515923:17518304:17518360:17519708:17519818 | 17518304:17518360 | ENSG00000006611.11 | ENST00000526313.1,ENST00000318024.4,ENST00000527720.1,ENST00000527020.1,ENST00000529563.1 |
| exon_skip_69610 | 11 | 17518304:17518360:17519708:17519818:17522597:17522694 | 17519708:17519818 | ENSG00000006611.11 | ENST00000526313.1,ENST00000318024.4,ENST00000527720.1,ENST00000527020.1,ENST00000529563.1,ENST00000005226.7 |
| exon_skip_69637 | 11 | 17523485:17523527:17538947:17539021:17542416:17542509 | 17538947:17539021 | ENSG00000006611.11 | ENST00000318024.4,ENST00000527720.1,ENST00000527020.1 |
| exon_skip_69658 | 11 | 17533448:17533601:17537787:17537837:17542416:17542509 | 17537787:17537837 | ENSG00000006611.11 | ENST00000005226.7 |
| exon_skip_69662 | 11 | 17535987:17536173:17537787:17537837:17538947:17539021 | 17537787:17537837 | ENSG00000006611.11 | ENST00000530700.1 |
| exon_skip_69663 | 11 | 17537787:17537837:17538947:17539021:17542416:17542509 | 17538947:17539021 | ENSG00000006611.11 | ENST00000530700.1 |
| exon_skip_69665 | 11 | 17544429:17544473:17544757:17544814:17544965:17545025 | 17544757:17544814 | ENSG00000006611.11 | ENST00000526313.1,ENST00000318024.4,ENST00000527720.1,ENST00000005226.7,ENST00000526181.1 |
| exon_skip_69666 | 11 | 17552700:17552839:17552945:17553089:17554801:17554869 | 17552945:17553089 | ENSG00000006611.11 | ENST00000526313.1,ENST00000318024.4,ENST00000527720.1,ENST00000527020.1,ENST00000005226.7,ENST00000526181.1 |
| exon_skip_69668 | 11 | 17552980:17553089:17554801:17554869:17565818:17565854 | 17554801:17554869 | ENSG00000006611.11 | ENST00000318024.4,ENST00000527020.1,ENST00000005226.7 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for USH1C |
| Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000318024 | 17518304 | 17518360 | Frame-shift |
| ENST00000318024 | 17519708 | 17519818 | Frame-shift |
| ENST00000318024 | 17538947 | 17539021 | Frame-shift |
| ENST00000318024 | 17554801 | 17554869 | Frame-shift |
| ENST00000318024 | 17544757 | 17544814 | In-frame |
| ENST00000318024 | 17552945 | 17553089 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000318024 | 17518304 | 17518360 | Frame-shift |
| ENST00000318024 | 17519708 | 17519818 | Frame-shift |
| ENST00000318024 | 17538947 | 17539021 | Frame-shift |
| ENST00000318024 | 17554801 | 17554869 | Frame-shift |
| ENST00000318024 | 17544757 | 17544814 | In-frame |
| ENST00000318024 | 17552945 | 17553089 | In-frame |
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Infer the effects of exon skipping event on protein functional features for USH1C |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000318024 | 2254 | 552 | 17552945 | 17553089 | 214 | 357 | 35 | 82 |
| ENST00000318024 | 2254 | 552 | 17544757 | 17544814 | 929 | 985 | 273 | 292 |
| Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000318024 | 2254 | 552 | 17552945 | 17553089 | 214 | 357 | 35 | 82 |
| ENST00000318024 | 2254 | 552 | 17544757 | 17544814 | 929 | 985 | 273 | 292 |
| Lost protein functional features of individual exon skipping events in TCGA. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Q9Y6N9 | 35 | 82 | 1 | 552 | Chain | ID=PRO_0000065727;Note=Harmonin |
| Q9Y6N9 | 35 | 82 | 20 | 36 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3K1R |
| Q9Y6N9 | 35 | 82 | 39 | 46 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3K1R |
| Q9Y6N9 | 35 | 82 | 53 | 56 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3K1R |
| Q9Y6N9 | 35 | 82 | 57 | 62 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3K1R |
| Q9Y6N9 | 35 | 82 | 63 | 65 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3K1R |
| Q9Y6N9 | 35 | 82 | 68 | 70 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3K1R |
| Q9Y6N9 | 35 | 82 | 71 | 77 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3K1R |
| Q9Y6N9 | 35 | 82 | 1 | 86 | Region | Note=N-terminal domain;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20142502;Dbxref=PMID:20142502 |
| Q9Y6N9 | 35 | 82 | 47 | 49 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3K1R |
| Q9Y6N9 | 273 | 292 | 274 | 292 | Alternative sequence | ID=VSP_007422;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q9Y6N9 | 273 | 292 | 282 | 288 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1X5N |
| Q9Y6N9 | 273 | 292 | 1 | 552 | Chain | ID=PRO_0000065727;Note=Harmonin |
| Q9Y6N9 | 273 | 292 | 211 | 293 | Domain | Note=PDZ 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00143 |
| Q9Y6N9 | 273 | 292 | 273 | 280 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1X5N |
| Q9Y6N9 | 273 | 292 | 194 | 552 | Region | Note=Mediates interaction with MYO7B;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:26812017,ECO:0000269|PubMed:26812018;Dbxref=PMID:26812017,PMID:26812018 |
| Q9Y6N9 | 273 | 292 | 280 | 280 | Sequence conflict | Note=S->N;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9Y6N9 | 273 | 292 | 280 | 280 | Sequence conflict | Note=S->N;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9Y6N9 | 273 | 292 | 292 | 294 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1X5N |
| Lost protein functional features of individual exon skipping events in GTEx. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Q9Y6N9 | 35 | 82 | 1 | 552 | Chain | ID=PRO_0000065727;Note=Harmonin |
| Q9Y6N9 | 35 | 82 | 20 | 36 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3K1R |
| Q9Y6N9 | 35 | 82 | 39 | 46 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3K1R |
| Q9Y6N9 | 35 | 82 | 53 | 56 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3K1R |
| Q9Y6N9 | 35 | 82 | 57 | 62 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3K1R |
| Q9Y6N9 | 35 | 82 | 63 | 65 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3K1R |
| Q9Y6N9 | 35 | 82 | 68 | 70 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3K1R |
| Q9Y6N9 | 35 | 82 | 71 | 77 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3K1R |
| Q9Y6N9 | 35 | 82 | 1 | 86 | Region | Note=N-terminal domain;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20142502;Dbxref=PMID:20142502 |
| Q9Y6N9 | 35 | 82 | 47 | 49 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3K1R |
| Q9Y6N9 | 273 | 292 | 274 | 292 | Alternative sequence | ID=VSP_007422;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q9Y6N9 | 273 | 292 | 282 | 288 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1X5N |
| Q9Y6N9 | 273 | 292 | 1 | 552 | Chain | ID=PRO_0000065727;Note=Harmonin |
| Q9Y6N9 | 273 | 292 | 211 | 293 | Domain | Note=PDZ 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00143 |
| Q9Y6N9 | 273 | 292 | 273 | 280 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1X5N |
| Q9Y6N9 | 273 | 292 | 194 | 552 | Region | Note=Mediates interaction with MYO7B;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:26812017,ECO:0000269|PubMed:26812018;Dbxref=PMID:26812017,PMID:26812018 |
| Q9Y6N9 | 273 | 292 | 280 | 280 | Sequence conflict | Note=S->N;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9Y6N9 | 273 | 292 | 280 | 280 | Sequence conflict | Note=S->N;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9Y6N9 | 273 | 292 | 292 | 294 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1X5N |
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SNVs in the skipped exons for USH1C |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - Differential PSIs between mutated versus non-mutated samples. |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_69594 | 17517116 | 17517224 | 17517119 | 17517119 | Frame_Shift_Del | G | - | p.P884fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_69665 | 17544758 | 17544814 | 17544807 | 17544807 | Frame_Shift_Del | T | - | p.N276fs |
| READ | TCGA-AH-6644-01 | exon_skip_69666 | 17552946 | 17553089 | 17552956 | 17552957 | Frame_Shift_Del | GG | - | p.80_80del |
| STAD | TCGA-BR-6852-01 | exon_skip_69598 | 17518305 | 17518360 | 17518325 | 17518326 | Frame_Shift_Ins | - | G | p.P842fs |
| STAD | TCGA-BR-6852-01 | exon_skip_69598 | 17518305 | 17518360 | 17518326 | 17518327 | Frame_Shift_Ins | - | G | p.P542fs |
| PAAD | TCGA-PZ-A5RE-01 | exon_skip_69666 | 17552946 | 17553089 | 17552955 | 17552956 | Frame_Shift_Ins | - | G | p.A80fs |
| UCEC | TCGA-D1-A17M-01 | exon_skip_69594 | 17517116 | 17517224 | 17517181 | 17517181 | Nonsense_Mutation | G | A | p.R864* |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - Non-synonymous mutations located in the skipped exons in CCLE. |
| Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| HS840T_FIBROBLAST | 17518305 | 17518360 | 17518348 | 17518348 | Missense_Mutation | G | A | p.L535F |
| NCIH2342_LUNG | 17519709 | 17519818 | 17519727 | 17519727 | Missense_Mutation | C | A | p.K524N |
| EVSAT_BREAST | 17519709 | 17519818 | 17519730 | 17519730 | Missense_Mutation | C | G | p.Q523H |
| HEC59_ENDOMETRIUM | 17519709 | 17519818 | 17519738 | 17519738 | Missense_Mutation | C | T | p.A521T |
| JHU029_UPPER_AERODIGESTIVE_TRACT | 17519709 | 17519818 | 17519741 | 17519741 | Missense_Mutation | C | T | p.A520T |
| K2_SKIN | 17519709 | 17519818 | 17519757 | 17519758 | Missense_Mutation | GG | AA | p.T514I |
| PK1_PANCREAS | 17519709 | 17519818 | 17519762 | 17519762 | Missense_Mutation | A | C | p.Y513D |
| CHLA218_BONE | 17519709 | 17519818 | 17519798 | 17519798 | Missense_Mutation | C | T | p.E501K |
| NCIH1339_LUNG | 17519709 | 17519818 | 17519803 | 17519803 | Missense_Mutation | C | A | p.G499V |
| JHUEM7_ENDOMETRIUM | 17544758 | 17544814 | 17544775 | 17544775 | Missense_Mutation | A | G | p.S287P |
| HEC6_ENDOMETRIUM | 17544758 | 17544814 | 17544790 | 17544790 | Missense_Mutation | G | A | p.R282C |
| MCCAR_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 17552946 | 17553089 | 17552956 | 17552956 | Missense_Mutation | G | C | p.R80G |
| HCC1569_BREAST | 17552946 | 17553089 | 17553030 | 17553030 | Missense_Mutation | C | T | p.R55H |
| NCIH1417_LUNG | 17554802 | 17554869 | 17554826 | 17554826 | Missense_Mutation | T | C | p.Y27C |
| SCLC22H_LUNG | 17554802 | 17554869 | 17554830 | 17554830 | Missense_Mutation | G | T | p.L26I |
| SCLC21H_LUNG | 17554802 | 17554869 | 17554830 | 17554830 | Missense_Mutation | G | T | p.L26I |
| HEC251_ENDOMETRIUM | 17554802 | 17554869 | 17554815 | 17554815 | Nonsense_Mutation | G | A | p.R31* |
| IGR1_SKIN | 17518305 | 17518360 | 17518360 | 17518361 | Splice_Site | CC | TT | p.G531K |
| CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 17544758 | 17544814 | 17544813 | 17544813 | Splice_Site | G | T | p.A274D |
| CW2_LARGE_INTESTINE | 17552946 | 17553089 | 17552947 | 17552947 | Splice_Site | T | C | p.R83G |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for USH1C |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for USH1C |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for USH1C |
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RelatedDrugs for USH1C |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for USH1C |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| USH1C | C2931207 | Usher syndrome, type 1C | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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