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

Gene ID: 54102, updated on 5-Mar-2024

Summary

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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
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Genomic context

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See CLIC6 in Genome Data Viewer
Location:
21q22.12
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (34668994..34718223)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (33051578..33100790)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (36041293..36090521)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:35828103-35828603 Neighboring gene small nucleolar RNA SNORA11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:35831243-35832104 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:35832105-35832965 Neighboring gene potassium voltage-gated channel subfamily E regulatory subunit 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18395 Neighboring gene VISTA enhancer hs2084 Neighboring gene regulator of calcineurin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:35954416-35954916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:35954917-35955417 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13269 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13270 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18397 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18400 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18399 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13271 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13272 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13273 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:36095588-36096365 Neighboring gene uncharacterized LOC107985515 Neighboring gene long intergenic non-protein coding RNA 160 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:36118001-36118502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:36118503-36119002 Neighboring gene Sharpr-MPRA regulatory region 10169 Neighboring gene long intergenic non-protein coding RNA 1426

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: 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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Related articles in PubMed

  1. Proteomic landscape of the human choroid-retinal pigment epithelial complex. Skeie JM, et al. JAMA Ophthalmol, 2014 Nov. PMID 25058583
  2. Combined linkage analysis and exome sequencing identifies novel genes for familial goiter. Yan J, et al. J Hum Genet, 2013 Jun. PMID 23535966
  3. Detailed molecular and clinical characterization of three patients with 21q deletions. Lindstrand A, et al. Clin Genet, 2010 Feb. PMID 19863549
  4. Segmental paralogy in the human genome: a large-scale triplication on 1p, 6p, and 21q. Strippoli P, et al. Mamm Genome, 2002 Aug. PMID 12226712
  5. Identification of a novel member of the CLIC family, CLIC6, mapping to 21q22.12. Friedli M, et al. Gene, 2003 Nov 27. PMID 14597386

See all (18) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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 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 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
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)

  1. 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 ...

  2. 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 ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    34668994..34718223
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    33051578..33100790
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96NY7.3 GenPept UniProtKB/Swiss-Prot:Q96NY7

Gene LinkOut

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