U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

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

    Summary

    Go to the top of the page Help
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    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

    Go to the top of the page Help

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

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    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

    Go to the top of the page Help
    Preferred Names
    chloride intracellular channel protein 6
    Names
    chloride channel form A
    parchorin

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous