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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 CLCN3 |
 Gene summary |
| Gene information | Gene symbol | CLCN3 | Gene ID | 1182 |
| Gene name | chloride voltage-gated channel 3 | |
| Synonyms | CLC3|ClC-3 | |
| Cytomap | 4q33 | |
| Type of gene | protein-coding | |
| Description | H(+)/Cl(-) exchange transporter 3chloride channel 3chloride channel protein 3chloride channel, voltage-sensitive 3chloride transporter ClC-3 | |
| Modification date | 20180523 | |
| UniProtAcc | P51790 | |
| Context | PubMed: CLCN3 [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 |
| CLCN3 | GO:1902476 | chloride transmembrane transport | 11274166 |
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Exon skipping events across known transcript of Ensembl for CLCN3 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 CLCN3 |
| 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 CLCN3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_427061 | 4 | 170541987:170542214:170557063:170557239:170601200:170601358 | 170557063:170557239 | ENSG00000109572.9 | ENST00000513761.1,ENST00000347613.4,ENST00000360642.3 |
| exon_skip_427064 | 4 | 170557133:170557239:170584677:170584768:170601200:170601358 | 170584677:170584768 | ENSG00000109572.9 | ENST00000504131.2 |
| exon_skip_427070 | 4 | 170601218:170601358:170608808:170608908:170610193:170610296 | 170608808:170608908 | ENSG00000109572.9 | ENST00000507875.1,ENST00000513761.1,ENST00000347613.4,ENST00000511092.1,ENST00000504131.2,ENST00000360642.3 |
| exon_skip_427071 | 4 | 170613264:170613471:170616762:170616843:170618339:170618430 | 170616762:170616843 | ENSG00000109572.9 | ENST00000507875.1,ENST00000513761.1,ENST00000347613.4,ENST00000504131.2 |
| exon_skip_427074 | 4 | 170616781:170616843:170618339:170618430:170618511:170618885 | 170618339:170618430 | ENSG00000109572.9 | ENST00000515420.1 |
| exon_skip_427076 | 4 | 170618511:170618885:170625148:170625335:170628018:170628039 | 170625148:170625335 | ENSG00000109572.9 | ENST00000507875.1,ENST00000513761.1,ENST00000515420.1,ENST00000347613.4,ENST00000504131.2,ENST00000360642.3 |
| exon_skip_427079 | 4 | 170625148:170625335:170628018:170628417:170634229:170634338 | 170628018:170628417 | ENSG00000109572.9 | ENST00000507875.1,ENST00000513761.1,ENST00000347613.4,ENST00000504131.2,ENST00000360642.3 |
| exon_skip_427082 | 4 | 170634229:170634446:170638942:170639018:170641057:170641429 | 170638942:170639018 | ENSG00000109572.9 | ENST00000347613.4 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for CLCN3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_427061 | 4 | 170541987:170542214:170557063:170557239:170601200:170601358 | 170557063:170557239 | ENSG00000109572.9 | ENST00000513761.1,ENST00000347613.4,ENST00000360642.3 |
| exon_skip_427064 | 4 | 170557133:170557239:170584677:170584768:170601200:170601358 | 170584677:170584768 | ENSG00000109572.9 | ENST00000504131.2 |
| exon_skip_427070 | 4 | 170601218:170601358:170608808:170608908:170610193:170610296 | 170608808:170608908 | ENSG00000109572.9 | ENST00000511092.1,ENST00000513761.1,ENST00000347613.4,ENST00000360642.3,ENST00000504131.2,ENST00000507875.1 |
| exon_skip_427071 | 4 | 170613264:170613471:170616762:170616843:170618339:170618430 | 170616762:170616843 | ENSG00000109572.9 | ENST00000513761.1,ENST00000347613.4,ENST00000504131.2,ENST00000507875.1 |
| exon_skip_427074 | 4 | 170616781:170616843:170618339:170618430:170618511:170618885 | 170618339:170618430 | ENSG00000109572.9 | ENST00000515420.1 |
| exon_skip_427076 | 4 | 170618511:170618885:170625148:170625335:170628018:170628039 | 170625148:170625335 | ENSG00000109572.9 | ENST00000513761.1,ENST00000347613.4,ENST00000360642.3,ENST00000504131.2,ENST00000507875.1,ENST00000515420.1 |
| exon_skip_427079 | 4 | 170625148:170625335:170628018:170628417:170634229:170634338 | 170628018:170628417 | ENSG00000109572.9 | ENST00000513761.1,ENST00000347613.4,ENST00000360642.3,ENST00000504131.2,ENST00000507875.1 |
| exon_skip_427082 | 4 | 170634229:170634446:170638942:170639018:170641057:170641429 | 170638942:170639018 | ENSG00000109572.9 | ENST00000347613.4 |
| 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 CLCN3 |
| 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 |
| ENST00000513761 | 170557063 | 170557239 | 5CDS-5UTR |
| ENST00000513761 | 170608808 | 170608908 | Frame-shift |
| ENST00000513761 | 170625148 | 170625335 | Frame-shift |
| ENST00000513761 | 170616762 | 170616843 | In-frame |
| ENST00000513761 | 170628018 | 170628417 | 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 |
| ENST00000513761 | 170557063 | 170557239 | 5CDS-5UTR |
| ENST00000513761 | 170608808 | 170608908 | Frame-shift |
| ENST00000513761 | 170625148 | 170625335 | Frame-shift |
| ENST00000513761 | 170616762 | 170616843 | In-frame |
| ENST00000513761 | 170628018 | 170628417 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CLCN3 |
| 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 |
| ENST00000513761 | 6709 | 818 | 170616762 | 170616843 | 1496 | 1576 | 312 | 339 |
| ENST00000513761 | 6709 | 818 | 170628018 | 170628417 | 2310 | 2708 | 583 | 716 |
| 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 |
| ENST00000513761 | 6709 | 818 | 170616762 | 170616843 | 1496 | 1576 | 312 | 339 |
| ENST00000513761 | 6709 | 818 | 170628018 | 170628417 | 2310 | 2708 | 583 | 716 |
| 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 |
| P51790 | 312 | 339 | 312 | 338 | Alternative sequence | ID=VSP_045105;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P51790 | 312 | 339 | 1 | 818 | Chain | ID=PRO_0000094438;Note=H(+)/Cl(-) exchange transporter 3 |
| P51790 | 312 | 339 | 313 | 325 | Intramembrane | Note=Helical;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51790 | 312 | 339 | 329 | 337 | Intramembrane | Note=Helical;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51790 | 312 | 339 | 339 | 339 | Site | Note=Mediates proton transfer from the protein to the inner aqueous phase;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51790 | 583 | 716 | 630 | 630 | Binding site | Note=Chloride;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51790 | 583 | 716 | 1 | 818 | Chain | ID=PRO_0000094438;Note=H(+)/Cl(-) exchange transporter 3 |
| P51790 | 583 | 716 | 658 | 722 | Domain | Note=CBS 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00703 |
| P51790 | 583 | 716 | 572 | 586 | Intramembrane | Note=Helical;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51790 | 583 | 716 | 590 | 601 | Intramembrane | Note=Helical;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51790 | 583 | 716 | 602 | 605 | Intramembrane | Note=Note%3DLoop between two helices;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51790 | 583 | 716 | 689 | 691 | Nucleotide binding | Note=ATP;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51790 | 583 | 716 | 646 | 646 | Sequence conflict | Note=E->EEF;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P51790 | 583 | 716 | 646 | 646 | Sequence conflict | Note=E->EEF;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P51790 | 583 | 716 | 646 | 646 | Sequence conflict | Note=E->EEF;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P51790 | 583 | 716 | 625 | 818 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51790 | 583 | 716 | 606 | 624 | Transmembrane | Note=Helical;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| 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 |
| P51790 | 312 | 339 | 312 | 338 | Alternative sequence | ID=VSP_045105;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P51790 | 312 | 339 | 1 | 818 | Chain | ID=PRO_0000094438;Note=H(+)/Cl(-) exchange transporter 3 |
| P51790 | 312 | 339 | 313 | 325 | Intramembrane | Note=Helical;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51790 | 312 | 339 | 329 | 337 | Intramembrane | Note=Helical;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51790 | 312 | 339 | 339 | 339 | Site | Note=Mediates proton transfer from the protein to the inner aqueous phase;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51790 | 583 | 716 | 630 | 630 | Binding site | Note=Chloride;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51790 | 583 | 716 | 1 | 818 | Chain | ID=PRO_0000094438;Note=H(+)/Cl(-) exchange transporter 3 |
| P51790 | 583 | 716 | 658 | 722 | Domain | Note=CBS 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00703 |
| P51790 | 583 | 716 | 572 | 586 | Intramembrane | Note=Helical;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51790 | 583 | 716 | 590 | 601 | Intramembrane | Note=Helical;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51790 | 583 | 716 | 602 | 605 | Intramembrane | Note=Note%3DLoop between two helices;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51790 | 583 | 716 | 689 | 691 | Nucleotide binding | Note=ATP;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51790 | 583 | 716 | 646 | 646 | Sequence conflict | Note=E->EEF;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P51790 | 583 | 716 | 646 | 646 | Sequence conflict | Note=E->EEF;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P51790 | 583 | 716 | 646 | 646 | Sequence conflict | Note=E->EEF;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P51790 | 583 | 716 | 625 | 818 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51790 | 583 | 716 | 606 | 624 | Transmembrane | Note=Helical;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
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SNVs in the skipped exons for CLCN3 |
| - 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. |
CLCN3_BRCA_exon_skip_427061_psi_boxplot.png |
| - 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-DD-A39Y-01 | exon_skip_427070 | 170608809 | 170608908 | 170608847 | 170608847 | Frame_Shift_Del | A | - | p.T119fs |
| COAD | TCGA-AZ-4615-01 | exon_skip_427074 | 170618340 | 170618430 | 170618379 | 170618379 | Frame_Shift_Del | T | - | p.S352fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_427074 | 170618340 | 170618430 | 170618403 | 170618403 | Frame_Shift_Del | T | - | p.F361fs |
| LIHC | TCGA-KR-A7K0-01 | exon_skip_427074 | 170618340 | 170618430 | 170618424 | 170618424 | Frame_Shift_Del | C | - | p.N367fs |
| LIHC | TCGA-KR-A7K0-01 | exon_skip_427074 | 170618340 | 170618430 | 170618424 | 170618424 | Frame_Shift_Del | C | - | p.P368fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_427074 | 170618340 | 170618430 | 170618427 | 170618427 | Frame_Shift_Del | T | - | p.F369fs |
| STAD | TCGA-HU-A4H8-01 | exon_skip_427074 | 170618340 | 170618430 | 170618378 | 170618379 | Frame_Shift_Ins | - | T | p.S352fs |
| STAD | TCGA-HU-A4H8-01 | exon_skip_427074 | 170618340 | 170618430 | 170618379 | 170618380 | Frame_Shift_Ins | - | T | p.S352fs |
| BLCA | TCGA-FD-A3SR-01 | exon_skip_427070 | 170608809 | 170608908 | 170608906 | 170608906 | Nonsense_Mutation | C | A | p.S139* |
| BLCA | TCGA-ZF-A9R4-01 | exon_skip_427074 | 170618340 | 170618430 | 170618377 | 170618377 | Nonsense_Mutation | C | A | p.S352* |
| UCEC | TCGA-B5-A11N-01 | exon_skip_427079 | 170628019 | 170628417 | 170628207 | 170628207 | Nonsense_Mutation | G | T | p.E647* |
| THCA | TCGA-DJ-A13R-01 | exon_skip_427079 | 170628019 | 170628417 | 170628369 | 170628369 | Nonsense_Mutation | C | T | p.Q701* |
| THCA | TCGA-DJ-A13R-01 | exon_skip_427079 | 170628019 | 170628417 | 170628369 | 170628369 | Nonsense_Mutation | C | T | p.Q701X |
| BRCA | TCGA-AR-A1AR-01 | exon_skip_427061 | 170557064 | 170557239 | 170557240 | 170557240 | Splice_Site | G | T | e1+1 |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-AR-A1AR-01 |
| Cancer type: BRCA | |
| ESID: exon_skip_427061 | |
| Skipped exon start: 170557064 | |
| Skipped exon end: 170557239 | |
| Mutation start: 170557240 | |
| Mutation end: 170557240 | |
| Mutation type: Splice_Site | |
| Reference seq: G | |
| Mutation seq: T | |
| AAchange: e1+1 | |
exon_skip_427061_BRCA_TCGA-AR-A1AR-01.png | |
| - 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 |
| SW620_LARGE_INTESTINE | 170557064 | 170557239 | 170557155 | 170557155 | Missense_Mutation | G | A | p.E26K |
| OVK18_OVARY | 170557064 | 170557239 | 170557157 | 170557157 | Missense_Mutation | G | T | p.E26D |
| HCC2218_BREAST | 170608809 | 170608908 | 170608811 | 170608811 | Missense_Mutation | C | G | p.I107M |
| NCIH510_LUNG | 170608809 | 170608908 | 170608863 | 170608863 | Missense_Mutation | G | A | p.A125T |
| LS411N_LARGE_INTESTINE | 170608809 | 170608908 | 170608873 | 170608873 | Missense_Mutation | G | A | p.G128E |
| NCIH727_LUNG | 170616763 | 170616843 | 170616775 | 170616775 | Missense_Mutation | G | T | p.A317S |
| MZ7B_MATCHED_NORMAL_TISSUE | 170616763 | 170616843 | 170616778 | 170616778 | Missense_Mutation | T | C | p.S318P |
| 127399_SOFT_TISSUE | 170618340 | 170618430 | 170618385 | 170618385 | Missense_Mutation | G | T | p.A355S |
| BT16_SOFT_TISSUE | 170618340 | 170618430 | 170618385 | 170618385 | Missense_Mutation | G | T | p.A355S |
| C8166_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 170618340 | 170618430 | 170618385 | 170618385 | Missense_Mutation | G | T | p.A355S |
| CAL120_BREAST | 170625149 | 170625335 | 170625202 | 170625202 | Missense_Mutation | G | T | p.R539S |
| MERO83_LUNG | 170625149 | 170625335 | 170625245 | 170625245 | Missense_Mutation | G | A | p.D554N |
| SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 170625149 | 170625335 | 170625278 | 170625278 | Missense_Mutation | G | A | p.G565R |
| SNGM_ENDOMETRIUM | 170625149 | 170625335 | 170625321 | 170625321 | Missense_Mutation | C | T | p.A579V |
| P30OHK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 170628019 | 170628417 | 170628119 | 170628119 | Missense_Mutation | T | G | p.S617R |
| HEC265_ENDOMETRIUM | 170628019 | 170628417 | 170628135 | 170628135 | Missense_Mutation | G | T | p.A623S |
| 2313287_STOMACH | 170628019 | 170628417 | 170628250 | 170628250 | Missense_Mutation | G | A | p.R661Q |
| NCIH3122_LUNG | 170628019 | 170628417 | 170628351 | 170628351 | Missense_Mutation | A | G | p.I695V |
| NCIH1573_LUNG | 170608809 | 170608908 | 170608839 | 170608839 | Nonsense_Mutation | G | T | p.E117* |
| JHUEM7_ENDOMETRIUM | 170618340 | 170618430 | 170618377 | 170618377 | Nonsense_Mutation | C | A | p.S352* |
| MCF7_BREAST | 170625149 | 170625335 | 170625249 | 170625249 | Nonsense_Mutation | G | A | p.W555* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CLCN3 |
| 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 |
| exon_skip_427064 | 4 | 170557133:170557239:170584677:170584768:170601200:170601358 | 170584677:170584768 | ENST00000504131.2 | HNSC | rs34755939 | chr4:170584703 | C/G | 1.02e-03 |
| exon_skip_427064 | 4 | 170557133:170557239:170584677:170584768:170601200:170601358 | 170584677:170584768 | ENST00000504131.2 | LGG | rs34755939 | chr4:170584703 | C/G | 3.69e-03 |
| exon_skip_427064 | 4 | 170557133:170557239:170584677:170584768:170601200:170601358 | 170584677:170584768 | ENST00000504131.2 | KIRC | rs34755939 | chr4:170584703 | C/G | 3.00e-04 |
| exon_skip_427064 | 4 | 170557133:170557239:170584677:170584768:170601200:170601358 | 170584677:170584768 | ENST00000504131.2 | KIRC | rs34755939 | chr4:170584703 | C/G | 7.58e-04 |
| exon_skip_427064 | 4 | 170557133:170557239:170584677:170584768:170601200:170601358 | 170584677:170584768 | ENST00000504131.2 | LUAD | rs34755939 | chr4:170584703 | C/G | 1.79e-03 |
| exon_skip_427064 | 4 | 170557133:170557239:170584677:170584768:170601200:170601358 | 170584677:170584768 | ENST00000504131.2 | PCPG | rs34755939 | chr4:170584703 | C/G | 1.21e-04 |
| exon_skip_427064 | 4 | 170557133:170557239:170584677:170584768:170601200:170601358 | 170584677:170584768 | ENST00000504131.2 | STAD | rs34755939 | chr4:170584703 | C/G | 5.70e-04 |
| exon_skip_427064 | 4 | 170557133:170557239:170584677:170584768:170601200:170601358 | 170584677:170584768 | ENST00000504131.2 | THCA | rs34755939 | chr4:170584703 | C/G | 1.44e-03 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CLCN3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CLCN3 |
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RelatedDrugs for CLCN3 |
| 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 CLCN3 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| CLCN3 | C0017638 | Glioma | 1 | CTD_human |
| CLCN3 | C0038356 | Stomach Neoplasms | 1 | CTD_human |
| CLCN3 | C2931822 | Nasopharyngeal carcinoma | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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