CLIC1

chloride intracellular channel 1, the group of Chloride intracellular channels

Basic information

Region (hg38): 6:31730581-31739763

Links

ENSG00000213719 ∙ NCBI:1192 ∙ OMIM:602872 ∙ HGNC:2062 ∙ Uniprot:O00299 ∙ 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 CLIC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLIC1 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			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in CLIC1

This is a list of pathogenic ClinVar variants found in the CLIC1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-31730936-C-T		not specified	Uncertain significance (Jul 26, 2024)
6-31730948-T-C		not specified	Uncertain significance (Jul 19, 2023)
6-31730957-C-G		not specified	Uncertain significance (Mar 11, 2022)
6-31732260-G-A		not specified	Uncertain significance (May 30, 2024)
6-31732273-C-T		not specified	Likely benign (Dec 03, 2021)
6-31732311-G-T		not specified	Uncertain significance (Sep 04, 2024)
6-31732327-C-G		not specified	Uncertain significance (Aug 05, 2024)
6-31732367-C-G		not specified	Uncertain significance (Feb 06, 2023)
6-31732371-A-G		not specified	Uncertain significance (Sep 13, 2023)
6-31733672-C-A		not specified	Uncertain significance (Nov 08, 2022)
6-31733872-A-G		not specified	Uncertain significance (Dec 26, 2023)
6-31733927-C-A		not specified	Uncertain significance (Feb 23, 2023)
6-31733929-C-A		not specified	Uncertain significance (Jan 19, 2024)
6-31734241-A-G		not specified	Uncertain significance (Dec 20, 2021)
6-31736267-C-T		not specified	Uncertain significance (Jan 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLIC1	protein_coding	protein_coding	ENST00000375780	6	9183

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000193	0.732	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.43	83	129	0.645	0.00000667	1559
Missense in Polyphen		19	29.131	0.65222		441
Synonymous	0.755	49	56.2	0.872	0.00000309	482
Loss of Function	0.971	7	10.4	0.675	4.36e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000662	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Can insert into membranes and form chloride ion channels. Channel activity depends on the pH. Membrane insertion seems to be redox-regulated and may occur only under oxydizing conditions. Involved in regulation of the cell cycle. {ECO:0000269|PubMed:10834939, ECO:0000269|PubMed:11195932, ECO:0000269|PubMed:11551966, ECO:0000269|PubMed:11940526, ECO:0000269|PubMed:11978800, ECO:0000269|PubMed:14613939, ECO:0000269|PubMed:9139710}.

Intolerance Scores

• loftool: 0.517
• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.487
• hipred: N
• hipred_score: 0.260
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Clic1
• Phenotype: homeostasis/metabolism phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: chloride transport;signal transduction;regulation of ion transmembrane transport;positive regulation of osteoblast differentiation;regulation of cell cycle;regulation of mitochondrial membrane potential;platelet aggregation;chloride transmembrane transport
• Cellular component: extracellular space;nucleus;nuclear envelope;cytoplasm;mitochondrion;plasma membrane;brush border;membrane;nuclear membrane;vesicle;chloride channel complex;perinuclear region of cytoplasm;extracellular exosome;blood microparticle
• Molecular function: voltage-gated ion channel activity;chloride channel activity;protein binding;cadherin binding