CLIC3

chloride intracellular channel 3, the group of Chloride intracellular channels

Basic information

Region (hg38): 9:136994608-136996568

Links

ENSG00000169583 ∙ NCBI:9022 ∙ OMIM:606533 ∙ HGNC:2064 ∙ Uniprot:O95833 ∙ 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 CLIC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLIC3 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in CLIC3

This is a list of pathogenic ClinVar variants found in the CLIC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-136994695-C-T		not specified	Uncertain significance (Aug 17, 2021)
9-136994701-G-A		not specified	Uncertain significance (Apr 08, 2023)
9-136994743-A-G		not specified	Uncertain significance (Nov 18, 2022)
9-136994782-G-T		not specified	Uncertain significance (Feb 17, 2024)
9-136994793-C-T		not specified	Uncertain significance (Jan 09, 2024)
9-136994800-C-T		not specified	Uncertain significance (May 15, 2023)
9-136994830-C-T		not specified	Uncertain significance (May 18, 2022)
9-136994835-A-G		not specified	Uncertain significance (Dec 05, 2022)
9-136994944-G-T		not specified	Uncertain significance (Dec 13, 2021)
9-136994949-G-A		not specified	Uncertain significance (Dec 06, 2022)
9-136995030-G-A		not specified	Uncertain significance (Feb 27, 2024)
9-136995057-A-G		not specified	Uncertain significance (Jun 04, 2024)
9-136995216-T-G		not specified	Uncertain significance (Jun 27, 2022)
9-136995291-A-T		not specified	Uncertain significance (May 16, 2023)
9-136995448-G-A		not specified	Uncertain significance (Oct 26, 2022)
9-136995526-A-C		not specified	Uncertain significance (Sep 23, 2023)
9-136995681-A-G		not specified	Uncertain significance (Jul 11, 2023)
9-136995686-C-A		not specified	Uncertain significance (Aug 30, 2022)
9-136995736-C-T		not specified	Uncertain significance (Oct 26, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLIC3	protein_coding	protein_coding	ENST00000494426	6	2169

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.23e-9	0.0385	125265	0	20	125285	0.0000798

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	116	156	0.742	0.0000114	1496
Missense in Polyphen		41	55.466	0.73919		622
Synonymous	2.30	52	77.8	0.668	0.00000621	481
Loss of Function	-0.889	11	8.25	1.33	3.93e-7	101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000369	0.000367
Ashkenazi Jewish	0.0000999	0.0000996
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000268	0.0000265
Middle Eastern	0.000109	0.000109
South Asian	0.0000654	0.0000653
Other	0.000164	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Can insert into membranes and form chloride ion channels. May participate in cellular growth control. {ECO:0000269|PubMed:9880541}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.560
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

• pHI: 0.488
• hipred: N
• hipred_score: 0.309
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.862

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clic3

Gene ontology

• Biological process: chloride transport;signal transduction;regulation of ion transmembrane transport;chloride transmembrane transport
• Cellular component: nucleus;cytoplasm;nuclear body;chloride channel complex;extracellular exosome
• Molecular function: voltage-gated ion channel activity;chloride channel activity;protein binding