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

    Gene ID: 1185, updated on 27-Nov-2024

    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; AllianceGenome:HGNC:2024
    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; CONRIBA
    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
    NEW
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    Try the new Transcript table

    Genomic context

    See CLCN6 in Genome Data Viewer
    Location:
    1p36.22
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (11806191..11843130)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (11350275..11387211)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (11866248..11903187)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene chromosome 1 open reading frame 167 Neighboring gene C1orf167 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:11847781-11848588 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:11851353-11851865 Neighboring gene methylenetetrahydrofolate reductase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:11860626-11861224 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:11862804-11863700 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:11863701-11864596 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 272 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 273 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:11865893-11866878 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 178 Neighboring gene NPPA antisense RNA 1 Neighboring gene VISTA enhancer hs2123 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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Neurodegeneration, childhood-onset, with hypotonia, respiratory insufficiency, and brain imaging abnormalities
    MedGen: C5543020 OMIM: 619173 GeneReviews: Not available
    not available

    EBI 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.
    EBI GWAS Catalog
    Genome-wide association study identifies eight loci associated with blood pressure.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA0046

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables antiporter activity TAS
    Traceable Author Statement
    more info
     
    enables chloride transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables voltage-gated chloride channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables voltage-gated chloride channel activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cell volume homeostasis NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in chloride transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chloride transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in chloride transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in monoatomic ion transmembrane transport TAS
    Traceable Author Statement
    more info
     
    involved_in response to mechanical stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in signal transduction NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in endosome membrane TAS
    Traceable Author Statement
    more info
     
    is_active_in intracellular membrane-bounded organelle IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in late endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in lysosomal membrane HDA PubMed 
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    H(+)/Cl(-) exchange transporter 6
    Names
    chloride channel, voltage-sensitive 6
    chloride transport protein 6

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_008766.2 RefSeqGene

      Range
      5002..41941
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001256959.2NP_001243888.2  H(+)/Cl(-) exchange transporter 6 isoform 2

      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)
      AL021155, AL953897
      Consensus CDS
      CCDS57972.1
      Related
      ENSP00000308367.7, ENST00000312413.10
      Conserved Domains (2) summary
      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:578834
      CBS_pair_voltage-gated_CLC_euk_bac; Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the voltage gated CLC (chloride channel) in eukaryotes and bacteria
    2. NM_001286.5NP_001277.2  H(+)/Cl(-) exchange transporter 6 isoform 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, AL953897
      Consensus CDS
      CCDS138.1
      UniProtKB/Swiss-Prot
      A8K1T4, B4DGT7, F8W9R3, O60818, O60819, O60820, O60821, P51797, P78520, P78521, Q17R81, Q5SNW2, Q5SNW3, Q5SNX1, Q5SNX2, Q5SNX3, Q99427, Q99428, Q99429
      Related
      ENSP00000234488.9, ENST00000346436.11
      Conserved Domains (2) summary
      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:600856
      CBS_pair_voltage-gated_CLC_euk_bac; Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the voltage gated CLC (chloride channel) in eukaryotes and bacteria

    RNA

    1. NR_046428.2 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, AL953897

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      11806191..11843130
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      11350275..11387211
      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.