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    CLCN6 chloride voltage-gated channel 6 [ Homo sapiens (human) ]

    Gene ID: 1185, updated on 12-Aug-2018

    Summary

    Official Symbol
    CLCN6provided by HGNC
    Official Full Name
    chloride voltage-gated channel 6provided by HGNC
    Primary source
    HGNC:HGNC:2024
    See related
    Ensembl:ENSG00000011021 MIM:602726; Vega:OTTHUMG00000002299
    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
    CLC-6
    Summary
    This gene encodes a member of the voltage-dependent chloride channel protein family. Members of this family can function as either chloride channels or antiporters. This protein is primarily localized to late endosomes and functions as a chloride/proton antiporter. Alternate splicing results in both coding and non-coding variants. Additional alternately spliced variants have been described but their full-length structure is unknown. [provided by RefSeq, Mar 2012]
    Expression
    Ubiquitous expression in brain (RPKM 13.0), testis (RPKM 10.2) and 24 other tissues See more
    Orthologs

    Genomic context

    See CLCN6 in Genome Data Viewer
    Location:
    1p36.22
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (11806096..11843144)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (11866153..11903201)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene atrophin-1-like Neighboring gene chromosome 1 open reading frame 167 Neighboring gene uncharacterized LOC102724659 Neighboring gene methylenetetrahydrofolate reductase Neighboring gene NPPA antisense RNA 1 Neighboring gene natriuretic peptide A Neighboring gene natriuretic peptide B

    Genomic regions, transcripts, and products

    Expression

    • 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 Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    NHGRI GWAS Catalog

    Description
    Genome-wide association analysis and fine mapping of NT-proBNP level provide novel insight into the role of the MTHFR-CLCN6-NPPA-NPPB gene cluster.
    NHGRI GWA Catalog
    Genome-wide association study identifies eight loci associated with blood pressure.
    NHGRI GWA Catalog

    Pathways from BioSystems

    • Disease, organism-specific biosystem (from REACTOME)
      Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
    • Diseases of signal transduction, organism-specific biosystem (from REACTOME)
      Diseases of signal transduction, organism-specific biosystemSignaling processes are central to human physiology (e.g., Pires-da Silva & Sommer 2003), and their disruption by either germ-line and somatic mutation can lead to serious disease. Here, the molecula...
    • Ion channel transport, organism-specific biosystem (from REACTOME)
      Ion channel transport, organism-specific biosystemIon channels mediate the flow of ions across the plasma membrane of cells. They are integral membrane proteins, typically a multimer of proteins, which, when arranged in the membrane, create a pore f...
    • Oncogenic MAPK signaling, organism-specific biosystem (from REACTOME)
      Oncogenic MAPK signaling, organism-specific biosystemThe importance of the RAS/RAF/MAPK cascade in regulating cellular proliferation, differentiation and survival is highlighted by the fact that components of the pathway are mutated with high frequency...
    • Signaling by BRAF and RAF fusions, organism-specific biosystem (from REACTOME)
      Signaling by BRAF and RAF fusions, organism-specific biosystemIn addition to the more prevalent point mutations, BRAF and RAF1 are also subject to activation as a result of translocation events that yield truncated or fusion products (Jones et al, 2008; Cin et ...
    • Stimuli-sensing channels, organism-specific biosystem (from REACTOME)
      Stimuli-sensing channels, organism-specific biosystemIon channels that mediate sensations such as pain, warmth, cold, taste pressure and vision. Channels that mediate these sensations include acid-sensing ion channels (ASICs) (Wang & Xu 2011, Qadri et ...
    • Transmembrane transport of small molecules, organism-specific biosystem (from REACTOME)
      Transmembrane transport of small molecules, organism-specific biosystem
      Transmembrane transport of small molecules

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • KIAA0046

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    antiporter activity TAS
    Traceable Author Statement
    more info
     
    protein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    voltage-gated chloride channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    voltage-gated chloride channel activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    cell volume homeostasis NAS
    Non-traceable Author Statement
    more info
    PubMed 
    chloride transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    chloride transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    ion transmembrane transport TAS
    Traceable Author Statement
    more info
     
    response to mechanical stimulus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    response to mechanical stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    signal transduction NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    endosome membrane TAS
    Traceable Author Statement
    more info
     
    integral component of membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    lysosomal membrane HDA PubMed 

    General protein information

    Preferred Names
    chloride transport protein 6
    Names
    chloride channel, voltage-sensitive 6

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_008766.1 RefSeqGene

      Range
      4947..41995
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001256959.1NP_001243888.1  chloride transport protein 6 isoform 2

      See identical proteins and their annotated locations for NP_001243888.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AK294764, AL021155, DA229615, R20538
      Consensus CDS
      CCDS57972.1
      UniProtKB/Swiss-Prot
      P51797
      Related
      ENSP00000308367.7, ENST00000312413.10
      Conserved Domains (5) summary
      smart00116
      Location:586633
      CBS; Domain in cystathionine beta-synthase and other proteins
      COG0517
      Location:781831
      CBS; CBS domain [Signal transduction mechanisms]
      cd03685
      Location:40566
      ClC_6_like; ClC-6-like chloride channel proteins. This CD includes ClC-6, ClC-7 and ClC-B, C, D in plants. Proteins in this family are ubiquitous in eukarotes and their functions are unclear. They are expressed in intracellular organelles membranes. This family ...
      cd04591
      Location:679831
      CBS_pair_EriC_assoc_euk_bac; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in eukaryotes and bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of ...
      pfam00654
      Location:118548
      Voltage_CLC; Voltage gated chloride channel
    2. NM_001286.3NP_001277.1  chloride transport protein 6 isoform 1

      See identical proteins and their annotated locations for NP_001277.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) is the longest transcript and encodes the longer isoform (1). This isoform is also known as CLC-6a.
      Source sequence(s)
      AL021155, D28475, DA229615, R20538
      Consensus CDS
      CCDS138.1
      UniProtKB/Swiss-Prot
      P51797
      Related
      ENSP00000234488.9, OTTHUMP00000002410, ENST00000346436.10, OTTHUMT00000006639
      Conserved Domains (3) summary
      smart00116
      Location:608655
      CBS; Domain in cystathionine beta-synthase and other proteins
      cd03685
      Location:49588
      ClC_6_like; ClC-6-like chloride channel proteins. This CD includes ClC-6, ClC-7 and ClC-B, C, D in plants. Proteins in this family are ubiquitous in eukarotes and their functions are unclear. They are expressed in intracellular organelles membranes. This family ...
      cd04591
      Location:701853
      CBS_pair_EriC_assoc_euk_bac; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in eukaryotes and bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of ...

    RNA

    1. NR_046428.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL021155, BC143844, D28475, DA229615, R20538

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

      Range
      11806096..11843144
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_021735.2: Suppressed sequence

      Description
      NM_021735.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    2. NM_021736.2: Suppressed sequence

      Description
      NM_021736.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    3. NM_021737.2: Suppressed sequence

      Description
      NM_021737.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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