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    CLCNKA chloride voltage-gated channel Ka [ Homo sapiens (human) ]

    Gene ID: 1187, updated on 20-Dec-2019

    Summary

    Official Symbol
    CLCNKAprovided by HGNC
    Official Full Name
    chloride voltage-gated channel Kaprovided by HGNC
    Primary source
    HGNC:HGNC:2026
    See related
    Ensembl:ENSG00000186510 MIM:602024
    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
    CLCK1; ClC-K1; hClC-Ka
    Summary
    This gene is a member of the CLC family of voltage-gated chloride channels. The encoded protein is predicted to have 12 transmembrane domains, and requires a beta subunit called barttin to form a functional channel. It is thought to function in salt reabsorption in the kidney and potassium recycling in the inner ear. The gene is highly similar to CLCNKB, which is located 10 kb downstream from this gene. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in kidney (RPKM 55.9), salivary gland (RPKM 4.5) and 1 other tissue See more
    Orthologs

    Genomic context

    See CLCNKA in Genome Data Viewer
    Location:
    1p36.13
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    109.20191205 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (16022036..16034050)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (16348486..16360548)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene steroid receptor associated and regulated protein Neighboring gene heat shock protein family B (small) member 7 Neighboring gene CLCNKA recombination region Neighboring gene family with sequence similarity 131 member C pseudogene Neighboring gene CLCNKB recombination region Neighboring gene chloride voltage-gated channel Kb

    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?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Potential readthrough

    Included gene: SPEN

    Homology

    Clone Names

    • MGC61490

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    voltage-gated chloride channel activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    chloride transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    excretion TAS
    Traceable Author Statement
    more info
    PubMed 
    ion transmembrane transport TAS
    Traceable Author Statement
    more info
     
    regulation of ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    chloride channel complex IEA
    Inferred from Electronic Annotation
    more info
     
    integral component of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    chloride channel protein ClC-Ka
    Names
    chloride channel Ka
    chloride channel, kidney, A
    chloride channel, voltage-sensitive Ka

    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_009359.1 RefSeqGene

      Range
      5046..17060
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001042704.2NP_001036169.1  chloride channel protein ClC-Ka isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in a protein (isoform 2) that is one amino acid shorter than isoform 1.
      Source sequence(s)
      AK225550, BC053869
      Consensus CDS
      CCDS41269.1
      UniProtKB/Swiss-Prot
      P51800
      Related
      ENSP00000364844.1, ENST00000375692.5
      Conserved Domains (3) summary
      cd03683
      Location:49534
      ClC_1_like; ClC-1-like chloride channel proteins. This CD includes isoforms ClC-0, ClC-1, ClC-2 and ClC_K. ClC-1 is expressed in skeletal muscle and its mutation leads to both recessively and dominantly-inherited forms of muscle stiffness or myotonia. ClC-K is ...
      cd04591
      Location:555675
      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:106513
      Voltage_CLC; Voltage gated chloride channel
    2. NM_001257139.2NP_001244068.1  chloride channel protein ClC-Ka isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The resulting protein is shorter compared to isoform 1.
      Source sequence(s)
      AI821546, AK298285, AL355994
      Consensus CDS
      CCDS57973.1
      UniProtKB/Swiss-Prot
      P51800
      Related
      ENSP00000414445.2, ENST00000439316.6
      Conserved Domains (3) summary
      cd03683
      Location:49491
      ClC_1_like; ClC-1-like chloride channel proteins. This CD includes isoforms ClC-0, ClC-1, ClC-2 and ClC_K. ClC-1 is expressed in skeletal muscle and its mutation leads to both recessively and dominantly-inherited forms of muscle stiffness or myotonia. ClC-K is ...
      cd04591
      Location:512633
      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:59470
      Voltage_CLC; Voltage gated chloride channel
    3. NM_004070.4NP_004061.3  chloride channel protein ClC-Ka isoform 1

      See identical proteins and their annotated locations for NP_004061.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      BC053869, Z30643
      Consensus CDS
      CCDS167.1
      UniProtKB/Swiss-Prot
      P51800
      Related
      ENSP00000332771.4, ENST00000331433.5
      Conserved Domains (3) summary
      cd03683
      Location:49534
      ClC_1_like; ClC-1-like chloride channel proteins. This CD includes isoforms ClC-0, ClC-1, ClC-2 and ClC_K. ClC-1 is expressed in skeletal muscle and its mutation leads to both recessively and dominantly-inherited forms of muscle stiffness or myotonia. ClC-K is ...
      cd04591
      Location:555676
      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:106513
      Voltage_CLC; Voltage gated chloride channel

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

      Range
      16022036..16034050
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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