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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 CLCN4 |
 Gene summary |
| Gene information | Gene symbol | CLCN4 | Gene ID | 1183 |
| Gene name | chloride voltage-gated channel 4 | |
| Synonyms | CLC4|ClC-4|ClC-4A|MRX15|MRX49 | |
| Cytomap | Xp22.2 | |
| Type of gene | protein-coding | |
| Description | H(+)/Cl(-) exchange transporter 4chloride channel 4chloride channel protein 4chloride channel, voltage-sensitive 4chloride transporter ClC-4 | |
| Modification date | 20180523 | |
| UniProtAcc | P51793 | |
| Context | PubMed: CLCN4 [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 |
| CLCN4 | GO:0006821 | chloride transport | 10564087 |
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Exon skipping events across known transcript of Ensembl for CLCN4 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 CLCN4 |
| 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 CLCN4 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_509119 | X | 10126571:10126591:10153061:10153216:10155554:10155654 | 10153061:10153216 | ENSG00000073464.7 | ENST00000454850.1,ENST00000380829.1,ENST00000380833.4 |
| exon_skip_509121 | X | 10162950:10163138:10165978:10166101:10174397:10174604 | 10165978:10166101 | ENSG00000073464.7 | ENST00000380829.1,ENST00000380833.4,ENST00000421085.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for CLCN4 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_509119 | X | 10126571:10126591:10153061:10153216:10155554:10155654 | 10153061:10153216 | ENSG00000073464.7 | ENST00000380833.4,ENST00000380829.1,ENST00000454850.1 |
| exon_skip_509121 | X | 10162950:10163138:10165978:10166101:10174397:10174604 | 10165978:10166101 | ENSG00000073464.7 | ENST00000380833.4,ENST00000380829.1,ENST00000421085.2 |
| 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 CLCN4 |
| 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 |
| ENST00000380833 | 10153061 | 10153216 | 5CDS-5UTR |
| ENST00000380833 | 10165978 | 10166101 | 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 |
| ENST00000380833 | 10153061 | 10153216 | 5CDS-5UTR |
| ENST00000380833 | 10165978 | 10166101 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CLCN4 |
| 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 |
| ENST00000380833 | 6767 | 760 | 10165978 | 10166101 | 824 | 946 | 144 | 185 |
| 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 |
| ENST00000380833 | 6767 | 760 | 10165978 | 10166101 | 824 | 946 | 144 | 185 |
| 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 |
| P51793 | 144 | 185 | 181 | 181 | Binding site | Note=Chloride;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51793 | 144 | 185 | 1 | 760 | Chain | ID=PRO_0000094443;Note=H(+)/Cl(-) exchange transporter 4 |
| P51793 | 144 | 185 | 183 | 190 | Intramembrane | Note=Helical;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51793 | 144 | 185 | 180 | 184 | Motif | Note=Selectivity filter part_1;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51793 | 144 | 185 | 178 | 178 | Sequence conflict | Note=A->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P51793 | 144 | 185 | 151 | 174 | 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 |
| P51793 | 144 | 185 | 181 | 181 | Binding site | Note=Chloride;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51793 | 144 | 185 | 1 | 760 | Chain | ID=PRO_0000094443;Note=H(+)/Cl(-) exchange transporter 4 |
| P51793 | 144 | 185 | 183 | 190 | Intramembrane | Note=Helical;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51793 | 144 | 185 | 180 | 184 | Motif | Note=Selectivity filter part_1;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| P51793 | 144 | 185 | 178 | 178 | Sequence conflict | Note=A->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P51793 | 144 | 185 | 151 | 174 | Transmembrane | Note=Helical;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
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SNVs in the skipped exons for CLCN4 |
| - 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-DD-A3A0-01 | exon_skip_509121 | 10165979 | 10166101 | 10166039 | 10166039 | Frame_Shift_Del | T | - | p.F165fs |
| - 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 |
| HEP3B217_LIVER | 10153062 | 10153216 | 10153125 | 10153125 | Missense_Mutation | A | C | p.D18A |
| 639V_URINARY_TRACT | 10153062 | 10153216 | 10153157 | 10153157 | Missense_Mutation | G | C | p.D29H |
| CL34_LARGE_INTESTINE | 10153062 | 10153216 | 10153213 | 10153213 | Missense_Mutation | G | C | p.R47S |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CLCN4 |
| 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 CLCN4 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CLCN4 |
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RelatedDrugs for CLCN4 |
| 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 CLCN4 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| CLCN4 | C3887959 | MENTAL RETARDATION, X-LINKED 49 | 2 | UNIPROT |
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