CLIC6

chloride intracellular channel 6, the group of Chloride intracellular channels

Basic information

Region (hg38): 21:34668993-34718227

Previous symbols: [ "CLIC1L" ]

Links

ENSG00000159212 ∙ NCBI:54102 ∙ OMIM:615321 ∙ HGNC:2065 ∙ Uniprot:Q96NY7 ∙ 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 CLIC6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLIC6 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				9	3	12
missense			52	4	6	62
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	13	10

Variants in CLIC6

This is a list of pathogenic ClinVar variants found in the CLIC6 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-34669426-G-A		not specified	Uncertain significance (Aug 09, 2021)
21-34669477-A-T		not specified	Uncertain significance (Mar 24, 2023)
21-34669516-G-C		not specified	Likely benign (Nov 17, 2023)
21-34669521-G-C		not specified	Uncertain significance (Dec 06, 2021)
21-34669566-G-T		not specified	Uncertain significance (Aug 02, 2021)
21-34669615-C-T		not specified	Uncertain significance (Dec 13, 2022)
21-34669618-G-C		not specified	Uncertain significance (Jan 04, 2024)
21-34669629-G-A		not specified	Uncertain significance (Jun 06, 2022)
21-34669636-C-T		not specified	Uncertain significance (Nov 17, 2023)
21-34669671-G-A		not specified	Uncertain significance (Dec 06, 2022)
21-34669698-G-A		not specified	Likely benign (Feb 27, 2023)
21-34669725-C-T		not specified	Uncertain significance (Nov 14, 2023)
21-34669803-G-A		not specified	Uncertain significance (Oct 03, 2023)
21-34669836-G-A		not specified	Uncertain significance (May 28, 2024)
21-34669859-G-A			Likely benign (Apr 01, 2024)
21-34669864-G-A		not specified	Uncertain significance (Mar 29, 2023)
21-34669898-A-G		not specified	Uncertain significance (Sep 16, 2021)
21-34669919-C-G			Likely benign (Dec 31, 2019)
21-34669926-G-T			Benign (Jul 04, 2018)
21-34669928-A-G			Likely benign (Jul 17, 2018)
21-34669963-C-A		not specified	Uncertain significance (Jan 24, 2024)
21-34669997-G-C		not specified	Uncertain significance (Apr 25, 2022)
21-34670029-G-T		sellar metastasis from primary bronchial carcinoid tumor	Uncertain significance (Feb 06, 2020)
21-34670039-G-C			Likely benign (Jan 01, 2024)
21-34670043-A-G		not specified	Uncertain significance (Apr 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLIC6	protein_coding	protein_coding	ENST00000349499	6	48838

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000353	0.830	125708	0	39	125747	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.681	220	250	0.879	0.0000132	4341
Missense in Polyphen		95	106.16	0.89489		1417
Synonymous	-0.344	112	107	1.04	0.00000660	1378
Loss of Function	1.30	9	14.3	0.628	6.13e-7	247

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000275	0.000275
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000185	0.000185
Middle Eastern	0.000326	0.000326
South Asian	0.000230	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May insert into membranes and form chloride ion channels. May play a critical role in water-secreting cells, possibly through the regulation of chloride ion transport (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.131

Haploinsufficiency Scores

• pHI: 0.0892
• hipred: N
• hipred_score: 0.247

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.390

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clic6

Zebrafish Information Network

• Gene name: clic6
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: regulation of ion transmembrane transport;chloride transmembrane transport
• Cellular component: cytoplasm;plasma membrane;chloride channel complex;extracellular exosome
• Molecular function: voltage-gated ion channel activity;chloride channel activity;D2 dopamine receptor binding;D3 dopamine receptor binding;D4 dopamine receptor binding