CLIC4

chloride intracellular channel 4, the group of Chloride intracellular channels

Basic information

Region (hg38): 1:24745382-24844321

Links

ENSG00000169504 ∙ NCBI:25932 ∙ OMIM:606536 ∙ HGNC:13518 ∙ Uniprot:Q9Y696 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CLIC4 gene.

• not_specified (19 variants)
• Short_stature (1 variants)

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. These statistics are base on transcript: NM_000013943.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense		1	21			22
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2			2
Total	0	1	23	0	0

GnomAD

Source: gnomAD

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
		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: dbNSFP

• 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

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

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