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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 CLCNKA |
 Gene summary |
| Gene information | Gene symbol | CLCNKA | Gene ID | 1187 |
| Gene name | chloride voltage-gated channel Ka | |
| Synonyms | CLCK1|ClC-K1|hClC-Ka | |
| Cytomap | 1p36.13 | |
| Type of gene | protein-coding | |
| Description | chloride channel protein ClC-Kachloride channel Kachloride channel, kidney, Achloride channel, voltage-sensitive Ka | |
| Modification date | 20180523 | |
| UniProtAcc | P51800 | |
| Context | PubMed: CLCNKA [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 |
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Exon skipping events across known transcript of Ensembl for CLCNKA 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 CLCNKA |
| 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 CLCNKA |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_1797 | 1 | 16346530:16346728:16347525:16347589:16347791:16348008 | 16347525:16347589 | ENSG00000186510.7 | ENST00000464764.1 |
| exon_skip_1798 | 1 | 16348546:16348558:16349107:16349214:16350294:16350409 | 16349107:16349214 | ENSG00000186510.7 | ENST00000464764.1,ENST00000375692.1,ENST00000420078.1,ENST00000439316.2,ENST00000331433.4,ENST00000495784.1 |
| exon_skip_1801 | 1 | 16350294:16350423:16351257:16351386:16352602:16352685 | 16351257:16351386 | ENSG00000186510.7 | ENST00000375692.1,ENST00000420078.1,ENST00000331433.4,ENST00000495784.1 |
| exon_skip_1802 | 1 | 16350294:16350423:16351353:16351386:16352602:16352685 | 16351353:16351386 | ENSG00000186510.7 | ENST00000464764.1 |
| exon_skip_1803 | 1 | 16353030:16353108:16353191:16353270:16353804:16353930 | 16353191:16353270 | ENSG00000186510.7 | ENST00000464764.1,ENST00000375692.1,ENST00000420078.1,ENST00000439316.2,ENST00000331433.4 |
| exon_skip_1804 | 1 | 16353804:16353930:16354315:16354400:16354512:16354614 | 16354315:16354400 | ENSG00000186510.7 | ENST00000491433.1,ENST00000464764.1,ENST00000375692.1,ENST00000420078.1,ENST00000439316.2,ENST00000331433.4 |
| exon_skip_1807 | 1 | 16354512:16354614:16355214:16355340:16355620:16355794 | 16355214:16355340 | ENSG00000186510.7 | ENST00000464764.1 |
| exon_skip_1808 | 1 | 16354512:16354614:16355255:16355340:16355620:16355794 | 16355255:16355340 | ENSG00000186510.7 | ENST00000491433.1,ENST00000375692.1,ENST00000420078.1,ENST00000439316.2,ENST00000331433.4 |
| exon_skip_1809 | 1 | 16356459:16356570:16356955:16357169:16358204:16358338 | 16356955:16357169 | ENSG00000186510.7 | ENST00000464764.1,ENST00000375692.1,ENST00000420078.1,ENST00000439316.2,ENST00000331433.4 |
| exon_skip_1816 | 1 | 16358940:16359021:16359664:16359751:16360105:16360158 | 16359664:16359751 | ENSG00000186510.7 | ENST00000464764.1,ENST00000375692.1,ENST00000420078.1,ENST00000439316.2,ENST00000331433.4 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for CLCNKA |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_1797 | 1 | 16346530:16346728:16347525:16347589:16347791:16348008 | 16347525:16347589 | ENSG00000186510.7 | ENST00000464764.1 |
| exon_skip_1801 | 1 | 16350294:16350423:16351257:16351386:16352602:16352685 | 16351257:16351386 | ENSG00000186510.7 | ENST00000375692.1,ENST00000495784.1,ENST00000420078.1,ENST00000331433.4 |
| exon_skip_1802 | 1 | 16350294:16350423:16351353:16351386:16352602:16352685 | 16351353:16351386 | ENSG00000186510.7 | ENST00000464764.1 |
| exon_skip_1803 | 1 | 16353030:16353108:16353191:16353270:16353804:16353930 | 16353191:16353270 | ENSG00000186510.7 | ENST00000464764.1,ENST00000375692.1,ENST00000420078.1,ENST00000439316.2,ENST00000331433.4 |
| exon_skip_1804 | 1 | 16353804:16353930:16354315:16354400:16354512:16354614 | 16354315:16354400 | ENSG00000186510.7 | ENST00000464764.1,ENST00000375692.1,ENST00000420078.1,ENST00000439316.2,ENST00000331433.4,ENST00000491433.1 |
| exon_skip_1807 | 1 | 16354512:16354614:16355214:16355340:16355620:16355794 | 16355214:16355340 | ENSG00000186510.7 | ENST00000464764.1 |
| exon_skip_1808 | 1 | 16354512:16354614:16355255:16355340:16355620:16355794 | 16355255:16355340 | ENSG00000186510.7 | ENST00000375692.1,ENST00000420078.1,ENST00000439316.2,ENST00000331433.4,ENST00000491433.1 |
| exon_skip_1809 | 1 | 16356459:16356570:16356955:16357169:16358204:16358338 | 16356955:16357169 | ENSG00000186510.7 | ENST00000464764.1,ENST00000375692.1,ENST00000420078.1,ENST00000439316.2,ENST00000331433.4 |
| exon_skip_1816 | 1 | 16358940:16359021:16359664:16359751:16360105:16360158 | 16359664:16359751 | ENSG00000186510.7 | ENST00000464764.1,ENST00000375692.1,ENST00000420078.1,ENST00000439316.2,ENST00000331433.4 |
| 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 CLCNKA |
| 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 |
| ENST00000331433 | 16349107 | 16349214 | 5CDS-5UTR |
| ENST00000331433 | 16353191 | 16353270 | Frame-shift |
| ENST00000331433 | 16354315 | 16354400 | Frame-shift |
| ENST00000331433 | 16355255 | 16355340 | Frame-shift |
| ENST00000331433 | 16356955 | 16357169 | Frame-shift |
| ENST00000331433 | 16351257 | 16351386 | In-frame |
| ENST00000331433 | 16359664 | 16359751 | 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 |
| ENST00000331433 | 16353191 | 16353270 | Frame-shift |
| ENST00000331433 | 16354315 | 16354400 | Frame-shift |
| ENST00000331433 | 16355255 | 16355340 | Frame-shift |
| ENST00000331433 | 16356955 | 16357169 | Frame-shift |
| ENST00000331433 | 16351257 | 16351386 | In-frame |
| ENST00000331433 | 16359664 | 16359751 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CLCNKA |
| 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 |
| ENST00000331433 | 2492 | 687 | 16351257 | 16351386 | 249 | 377 | 76 | 119 |
| ENST00000331433 | 2492 | 687 | 16359664 | 16359751 | 1949 | 2035 | 643 | 672 |
| 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 |
| ENST00000331433 | 2492 | 687 | 16351257 | 16351386 | 249 | 377 | 76 | 119 |
| ENST00000331433 | 2492 | 687 | 16359664 | 16359751 | 1949 | 2035 | 643 | 672 |
| 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 |
| P51800 | 76 | 119 | 77 | 119 | Alternative sequence | ID=VSP_044700;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P51800 | 76 | 119 | 1 | 687 | Chain | ID=PRO_0000094455;Note=Chloride channel protein ClC-Ka |
| P51800 | 76 | 119 | 80 | 80 | Natural variant | ID=VAR_063074;Note=In BARTS4B%3B a patient also carrying a mutation in CLCNKB. W->C;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15044642;Dbxref=dbSNP:rs121909137,PMID:15044642 |
| P51800 | 76 | 119 | 83 | 83 | Natural variant | ID=VAR_019787;Note=R->G;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.3;Dbxref=dbSNP:rs10927887 |
| P51800 | 643 | 672 | 654 | 660 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2PFI |
| P51800 | 643 | 672 | 663 | 669 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2PFI |
| P51800 | 643 | 672 | 1 | 687 | Chain | ID=PRO_0000094455;Note=Chloride channel protein ClC-Ka |
| P51800 | 643 | 672 | 626 | 684 | Domain | Note=CBS 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00703 |
| P51800 | 643 | 672 | 641 | 650 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2PFI |
| P51800 | 643 | 672 | 670 | 681 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2PFI |
| P51800 | 643 | 672 | 507 | 687 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| P51800 | 76 | 119 | 77 | 119 | Alternative sequence | ID=VSP_044700;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P51800 | 76 | 119 | 1 | 687 | Chain | ID=PRO_0000094455;Note=Chloride channel protein ClC-Ka |
| P51800 | 76 | 119 | 80 | 80 | Natural variant | ID=VAR_063074;Note=In BARTS4B%3B a patient also carrying a mutation in CLCNKB. W->C;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15044642;Dbxref=dbSNP:rs121909137,PMID:15044642 |
| P51800 | 76 | 119 | 83 | 83 | Natural variant | ID=VAR_019787;Note=R->G;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.3;Dbxref=dbSNP:rs10927887 |
| P51800 | 643 | 672 | 654 | 660 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2PFI |
| P51800 | 643 | 672 | 663 | 669 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2PFI |
| P51800 | 643 | 672 | 1 | 687 | Chain | ID=PRO_0000094455;Note=Chloride channel protein ClC-Ka |
| P51800 | 643 | 672 | 626 | 684 | Domain | Note=CBS 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00703 |
| P51800 | 643 | 672 | 641 | 650 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2PFI |
| P51800 | 643 | 672 | 670 | 681 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2PFI |
| P51800 | 643 | 672 | 507 | 687 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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SNVs in the skipped exons for CLCNKA |
| - 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_1798 | 16349108 | 16349214 | 16349129 | 16349129 | Frame_Shift_Del | G | - | p.V5fs |
| CESC | TCGA-EA-A3HU-01 | exon_skip_1798 | 16349108 | 16349214 | 16349179 | 16349179 | Frame_Shift_Del | G | - | p.G23fs |
| HNSC | TCGA-P3-A6T6-01 | exon_skip_1798 | 16349108 | 16349214 | 16349201 | 16349201 | Frame_Shift_Del | C | - | p.R30fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_1804 | 16354316 | 16354400 | 16354384 | 16354384 | Frame_Shift_Del | T | - | p.F285fs |
| COAD | TCGA-AZ-6598-01 | exon_skip_1808 exon_skip_1807 | 16355215 | 16355340 | 16355263 | 16355263 | Frame_Shift_Del | G | - | p.P325fs |
| COAD | TCGA-AZ-6598-01 | exon_skip_1808 exon_skip_1807 | 16355256 | 16355340 | 16355263 | 16355263 | Frame_Shift_Del | G | - | p.P325fs |
| UCEC | TCGA-A5-A0VQ-01 | exon_skip_1808 exon_skip_1807 | 16355215 | 16355340 | 16355263 | 16355263 | Frame_Shift_Del | G | - | p.V326fs |
| UCEC | TCGA-A5-A0VQ-01 | exon_skip_1808 exon_skip_1807 | 16355256 | 16355340 | 16355263 | 16355263 | Frame_Shift_Del | G | - | p.V326fs |
| UCEC | TCGA-D1-A101-01 | exon_skip_1798 | 16349108 | 16349214 | 16349176 | 16349177 | Frame_Shift_Ins | - | G | p.L21fs |
| UCEC | TCGA-D1-A0ZO-01 | exon_skip_1804 | 16354316 | 16354400 | 16354383 | 16354384 | Frame_Shift_Ins | - | T | p.F283fs |
| COAD | TCGA-AA-3663-01 | exon_skip_1803 | 16353192 | 16353270 | 16353271 | 16353271 | Splice_Site | G | A | . |
| - 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 |
| MEWO_SKIN | 16354316 | 16354400 | 16354331 | 16354344 | Frame_Shift_Del | TCTACAAGACCAGT | - | p.LYKTS266fs |
| MERO14_LUNG | 16349108 | 16349214 | 16349139 | 16349140 | Frame_Shift_Ins | - | A | p.E9fs |
| LNCAPCLONEFGC_PROSTATE | 16354316 | 16354400 | 16354335 | 16354336 | Frame_Shift_Ins | - | A | p.K268fs |
| NCIH1651_LUNG | 16349108 | 16349214 | 16349188 | 16349188 | Missense_Mutation | G | A | p.C25Y |
| NCIH650_LUNG | 16351258 | 16351386 | 16351266 | 16351266 | Missense_Mutation | T | A | p.W80R |
| SW1710_URINARY_TRACT | 16351258 | 16351386 | 16351295 | 16351295 | Missense_Mutation | C | A | p.H89Q |
| SNU1040_LARGE_INTESTINE | 16351258 | 16351386 | 16351312 | 16351312 | Missense_Mutation | C | T | p.S95F |
| HCC2450_LUNG | 16351354 | 16351386 | 16351358 | 16351358 | Missense_Mutation | C | A | p.F110L |
| HCC2450_LUNG | 16351258 | 16351386 | 16351358 | 16351358 | Missense_Mutation | C | A | p.F110L |
| EN_ENDOMETRIUM | 16353192 | 16353270 | 16353195 | 16353195 | Missense_Mutation | A | G | p.K194E |
| ASPC1_PANCREAS | 16353192 | 16353270 | 16353256 | 16353257 | Missense_Mutation | CA | GC | p.A214G |
| SNU1040_LARGE_INTESTINE | 16355256 | 16355340 | 16355266 | 16355266 | Missense_Mutation | T | C | p.Y327H |
| SNU1040_LARGE_INTESTINE | 16355215 | 16355340 | 16355266 | 16355266 | Missense_Mutation | T | C | p.Y327H |
| CP66MEL_SKIN | 16356956 | 16357169 | 16356989 | 16356989 | Missense_Mutation | C | T | p.T481I |
| PLCPRF5_LIVER | 16356956 | 16357169 | 16357066 | 16357066 | Missense_Mutation | G | T | p.A507S |
| MCAS_OVARY | 16356956 | 16357169 | 16357121 | 16357121 | Missense_Mutation | T | C | p.I525T |
| KPNSI9S_AUTONOMIC_GANGLIA | 16359665 | 16359751 | 16359717 | 16359717 | Missense_Mutation | G | C | p.R661P |
| IALM_LUNG | 16359665 | 16359751 | 16359717 | 16359717 | Missense_Mutation | G | C | p.R661P |
| NCIH1688_LUNG | 16359665 | 16359751 | 16359749 | 16359749 | Missense_Mutation | G | C | p.E672Q |
| CAL29_URINARY_TRACT | 16355256 | 16355340 | 16355285 | 16355285 | Nonsense_Mutation | T | A | p.L333* |
| CAL29_URINARY_TRACT | 16355215 | 16355340 | 16355285 | 16355285 | Nonsense_Mutation | T | A | p.L333* |
| NCIH820_LUNG | 16355256 | 16355340 | 16355340 | 16355340 | Splice_Site | G | C | p.R351R |
| NCIH820_LUNG | 16355215 | 16355340 | 16355340 | 16355340 | Splice_Site | G | C | p.R351R |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CLCNKA |
| 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 CLCNKA |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CLCNKA |
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RelatedDrugs for CLCNKA |
| 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 CLCNKA |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| CLCNKA | C0020538 | Hypertensive disease | 1 | CTD_human |
| CLCNKA | C2751312 | BARTTER SYNDROME, TYPE 4B | 1 | CTD_human;UNIPROT |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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