CLIC6 chloride intracellular channel 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CLIC6provided by HGNC
Official Full Name: chloride intracellular channel 6provided by HGNC
Primary source: HGNC:HGNC:2065
See related: Ensembl:ENSG00000159212 MIM:615321; AllianceGenome:HGNC:2065
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CLIC1L
Summary: This gene encodes a member of the chloride intracellular channel family of proteins. The gene is part of a large triplicated region found on chromosomes 1, 6, and 21. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Nov 2015]
Expression: Biased expression in stomach (RPKM 24.4), thyroid (RPKM 6.8) and 10 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 21q22.12

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	21	NC_000021.9 (34668994..34718223)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	21	NC_060945.1 (33051578..33100790)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	21	NC_000021.8 (36041293..36090521)

Chromosome 21 - NC_000021.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Observational study of gene-disease association. (HuGE Navigator)
Title: Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney aging.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS_CEB234 (e-PCR)
- UniSTS:255242

D21S65 (e-PCR)
- UniSTS:32298

SHGC-170123 (e-PCR)
- UniSTS:173750

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables D2 dopamine receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables D3 dopamine receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables D4 dopamine receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables chloride channel activity	IDA Inferred from Direct Assay more info	PubMed
enables oxidoreductase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in chloride transmembrane transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of chloride channel complex	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in extracellular exosome	HDA more info	PubMed
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: chloride intracellular channel protein 6

Names: chloride channel form A; glutaredoxin-like oxidoreductase CLIC6; parchorin

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001317009.2 → NP_001303938.1 chloride intracellular channel protein 6 isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AF448439, AK289663, AP000330, BC040196, CA442589

Consensus CDS

CCDS82669.1

UniProtKB/Swiss-Prot

A8K0U8, Q8IX31, Q96NY7

Related

ENSP00000353959.3, ENST00000360731.7

Conserved Domains (3) summary

TIGR00862
Location:471 → 704

O-ClC; intracellular chloride channel protein

cd10301
Location:563 → 702

GST_C_CLIC6; C-terminal, alpha helical domain of Chloride Intracellular Channel 6

cd03061
Location:471 → 556

GST_N_CLIC; GST_N family, Chloride Intracellular Channel (CLIC) subfamily; composed of CLIC1-5, p64, parchorin and similar proteins. They are auto-inserting, self-assembling intracellular anion channels involved in a wide variety of functions including regulated ...
NM_053277.3 → NP_444507.1 chloride intracellular channel protein 6 isoform 2

See identical proteins and their annotated locations for NP_444507.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AF448438, AK289663, AP000330, BC040196, CA442589

Consensus CDS

CCDS13638.1

UniProtKB/Swiss-Prot

Q96NY7

Related

ENSP00000290332.4, ENST00000349499.3

Conserved Domains (4) summary

TIGR00862
Location:453 → 686

O-ClC; intracellular chloride channel protein

cd10301
Location:545 → 684

GST_C_CLIC6; C-terminal, alpha helical domain of Chloride Intracellular Channel 6

PRK07764
Location:2 → 420

PRK07764; DNA polymerase III subunits gamma and tau; Validated

cd03061
Location:450 → 538

GST_N_CLIC; GST_N family, Chloride Intracellular Channel (CLIC) subfamily; composed of CLIC1-5, p64, parchorin and similar proteins. They are auto-inserting, self-assembling intracellular anion channels involved in a wide variety of functions including regulated ...