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    CLCN2 chloride voltage-gated channel 2 [ Homo sapiens (human) ]

    Gene ID: 1181, updated on 17-Jun-2019

    Summary

    Official Symbol
    CLCN2provided by HGNC
    Official Full Name
    chloride voltage-gated channel 2provided by HGNC
    Primary source
    HGNC:HGNC:2020
    See related
    Ensembl:ENSG00000114859 MIM:600570
    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
    CLC2; ECA2; ECA3; EGI3; EGMA; EJM6; EJM8; CIC-2; EGI11; HALD2; LKPAT; clC-2
    Summary
    This gene encodes a voltage-gated chloride channel. The encoded protein is a transmembrane protein that maintains chloride ion homeostasis in various cells. Defects in this gene may be a cause of certain epilepsies. Four transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2012]
    Expression
    Broad expression in testis (RPKM 8.7), colon (RPKM 7.2) and 24 other tissues See more
    Orthologs

    Genomic context

    See CLCN2 in Genome Data Viewer
    Location:
    3q27.1
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (184346185..184361605, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (184063973..184079439, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene proteasome 26S subunit, non-ATPase 2 Neighboring gene eukaryotic translation initiation factor 4 gamma 1 Neighboring gene small nucleolar RNA, C/D box 66 Neighboring gene family with sequence similarity 131 member A Neighboring gene RNA polymerase II subunit H Neighboring gene thrombopoietin

    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 FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    • 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...
    • Mineral absorption, organism-specific biosystem (from KEGG)
      Mineral absorption, organism-specific biosystemMinerals are one of the five fundamental groups of nutrients needed to sustain life. Of the minerals, calcium plays innumerable roles in our bodies, serving as a main component of bone as well as an ...
    • Mineral absorption, conserved biosystem (from KEGG)
      Mineral absorption, conserved biosystemMinerals are one of the five fundamental groups of nutrients needed to sustain life. Of the minerals, calcium plays innumerable roles in our bodies, serving as a main component of bone as well as an ...
    • 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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    voltage-gated chloride channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    cell differentiation involved in salivary gland development IEA
    Inferred from Electronic Annotation
    more info
     
    chloride transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    ion transmembrane transport TAS
    Traceable Author Statement
    more info
     
    regulation of aldosterone biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    retina development in camera-type eye 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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    chloride channel protein 2
    Names
    chloride channel 2
    chloride channel, voltage-sensitive 2

    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_016422.1 RefSeqGene

      Range
      4953..20419
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001171087.3NP_001164558.1  chloride channel protein 2 isoform 2

      See identical proteins and their annotated locations for NP_001164558.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AA524434, BC072004, DC403930
      Consensus CDS
      CCDS54691.1
      UniProtKB/Swiss-Prot
      P51788
      Related
      ENSP00000345056.7, ENST00000344937.11
      Conserved Domains (3) summary
      cd03683
      Location:90550
      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:773821
      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:143529
      Voltage_CLC; Voltage gated chloride channel
    2. NM_001171088.3NP_001164559.1  chloride channel protein 2 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AA524434, AC078797, AK302759, DC403930
      Consensus CDS
      CCDS54690.1
      UniProtKB/Swiss-Prot
      P51788
      Related
      ENSP00000400425.2, ENST00000434054.6
      Conserved Domains (3) summary
      cd03683
      Location:73523
      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:746794
      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:99502
      Voltage_CLC; Voltage gated chloride channel
    3. NM_001171089.3NP_001164560.1  chloride channel protein 2 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AA524434, AC078797, AK298952, DC403930
      Consensus CDS
      CCDS54692.1
      UniProtKB/Swiss-Prot
      P51788
      Related
      ENSP00000391928.1, ENST00000457512.1
      Conserved Domains (2) summary
      cd03683
      Location:90567
      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 ...
      pfam00654
      Location:143546
      Voltage_CLC; Voltage gated chloride channel
    4. NM_004366.6NP_004357.3  chloride channel protein 2 isoform 1

      See identical proteins and their annotated locations for NP_004357.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AA524434, AC078797, AF026004, DC403930
      Consensus CDS
      CCDS3263.1
      UniProtKB/Swiss-Prot
      P51788
      Related
      ENSP00000265593.4, ENST00000265593.9
      Conserved Domains (3) summary
      cd03683
      Location:90567
      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:790838
      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:143546
      Voltage_CLC; Voltage gated chloride channel

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

      Range
      184346185..184361605 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006713489.1XP_006713552.1  chloride channel protein 2 isoform X1

      See identical proteins and their annotated locations for XP_006713552.1

      Conserved Domains (3) summary
      cd03683
      Location:90567
      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:762803
      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:143546
      Voltage_CLC; Voltage gated chloride channel
    2. XM_006713490.2XP_006713553.1  chloride channel protein 2 isoform X3

      Conserved Domains (3) summary
      cd04591
      Location:404452
      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:46160
      Voltage_CLC; Voltage gated chloride channel
      cl02915
      Location:46181
      Voltage_gated_ClC; CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This ...
    3. XM_011512401.1XP_011510703.1  chloride channel protein 2 isoform X2

      Conserved Domains (2) summary
      cd03683
      Location:90567
      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 ...
      pfam00654
      Location:143546
      Voltage_CLC; Voltage gated chloride channel

    RNA

    1. XR_001740002.1 RNA Sequence

    2. XR_001740001.1 RNA Sequence

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