CLIC4
chloride intracellular channel 4, the group of Chloride intracellular channels
Basic information
Region (hg38): 1:24745382-24844321
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLIC4 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 0 |
Variants in CLIC4
This is a list of pathogenic ClinVar variants found in the CLIC4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-24814099-C-T | not specified | Uncertain significance (Jun 17, 2024) | ||
| 1-24814131-C-T | Short stature | Likely pathogenic (Nov 18, 2001) | ||
| 1-24814143-A-G | not specified | Uncertain significance (Feb 05, 2024) | ||
| 1-24814151-C-A | not specified | Uncertain significance (Dec 19, 2023) | ||
| 1-24814168-C-T | not specified | Uncertain significance (Jul 06, 2021) | ||
| 1-24827045-A-C | not specified | Uncertain significance (Oct 12, 2021) | ||
| 1-24840897-A-G | not specified | Uncertain significance (May 08, 2024) | ||
| 1-24840929-A-G | not specified | Uncertain significance (Sep 16, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CLIC4 | protein_coding | protein_coding | ENST00000374379 | 6 | 98968 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00109 | 0.843 | 125737 | 0 | 11 | 125748 | 0.0000437 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.792 | 105 | 130 | 0.805 | 0.00000615 | 1678 |
| Missense in Polyphen | 13 | 26.472 | 0.49109 | 329 | ||
| Synonymous | -0.302 | 53 | 50.3 | 1.05 | 0.00000252 | 464 |
| Loss of Function | 1.22 | 6 | 10.2 | 0.587 | 4.27e-7 | 147 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000185 | 0.000184 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000355 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000105 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Can insert into membranes and form poorly selective ion channels that may also transport chloride ions. Channel activity depends on the pH. Membrane insertion seems to be redox-regulated and may occur only under oxydizing conditions. Promotes cell- surface expression of HRH3. Has alternate cellular functions like a potential role in angiogenesis or in maintaining apical- basolateral membrane polarity during mitosis and cytokinesis. Could also promote endothelial cell proliferation and regulate endothelial morphogenesis (tubulogenesis). {ECO:0000269|PubMed:12163372, ECO:0000269|PubMed:14569596, ECO:0000269|PubMed:16176272, ECO:0000269|PubMed:16239224, ECO:0000269|PubMed:18302930, ECO:0000269|PubMed:19247789}.;
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- loftool
- 0.340
- rvis_EVS
- -0.23
- rvis_percentile_EVS
- 36.86
Haploinsufficiency Scores
- pHI
- 0.502
- hipred
- N
- hipred_score
- 0.439
- ghis
- 0.672
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.231
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Clic4
- Phenotype
- growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); vision/eye phenotype; immune system phenotype;
Gene ontology
- Biological process
- angiogenesis;endothelial cell morphogenesis;chloride transport;vacuolar acidification;fertilization;cell differentiation;keratinocyte differentiation;negative regulation of cell migration;regulation of ion transmembrane transport;establishment or maintenance of apical/basal cell polarity;multicellular organism growth;branching morphogenesis of an epithelial tube;regulation of cytoskeleton organization;retina vasculature morphogenesis in camera-type eye;cellular response to calcium ion;chloride transmembrane transport
- Cellular component
- nucleus;cytoplasm;mitochondrion;centrosome;cytosol;plasma membrane;microvillus;cell-cell junction;cell surface;actin cytoskeleton;microtubule cytoskeleton;nuclear matrix;midbody;cytoplasmic vesicle membrane;chloride channel complex;apical part of cell;perinuclear region of cytoplasm;extracellular exosome
- Molecular function
- voltage-gated ion channel activity;chloride channel activity;protein binding