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

Gene ID: 1181, updated on 1-Mar-2024

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; AllianceGenome:HGNC:2020
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; FHA2; FHII; 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
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Genomic context

See CLCN2 in Genome Data Viewer
Location:
3q27.1
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (184346185..184361605, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (187155451..187170873, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (184063973..184079393, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14959 Neighboring gene proteasome 26S subunit ubiquitin receptor, non-ATPase 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:184031817-184032317 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:184033042-184033663 Neighboring gene eukaryotic translation initiation factor 4 gamma 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:184045141-184045641 Neighboring gene small nucleolar RNA, C/D box 66 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20908 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:184053938-184054138 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:184055930-184056541 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20909 Neighboring gene family with sequence similarity 131 member A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:184061884-184062636 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:184062637-184063388 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:184063389-184064141 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:184064142-184064893 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:184077025-184077538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:184077539-184078050 Neighboring gene uncharacterized LOC124906311 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14964 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14965 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14966 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14967 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20910 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20911 Neighboring gene RNA polymerase II, I and III 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 Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables voltage-gated chloride channel activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables voltage-gated chloride channel activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in acinar cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in cell differentiation involved in salivary gland development IEA
Inferred from Electronic Annotation
more info
 
involved_in chloride transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
involved_in chloride transport IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in lung development IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of oligodendrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of aldosterone biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in retina development in camera-type eye 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 dendrite IEA
Inferred from Electronic Annotation
more info
 
located_in perikaryon IEA
Inferred from Electronic Annotation
more info
 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in 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)

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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
    4999..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
    B4DQT9, B4DZ58, E9PBD9, E9PCD2, O14864, P51788, Q6IPA9, Q8WU13
    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: 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_000003.12 Reference GRCh38.p14 Primary Assembly

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

mRNA and Protein(s)

  1. XM_006713489.2XP_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_011512401.2XP_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
  3. XM_047447419.1XP_047303375.1  chloride channel protein 2 isoform X3

    UniProtKB/TrEMBL
    A0A1B0GUY6
    Related
    ENSP00000490313.1, ENST00000636492.1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    187155451..187170873 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054345165.1XP_054201140.1  chloride channel protein 2 isoform X1

  2. XM_054345166.1XP_054201141.1  chloride channel protein 2 isoform X2

  3. XM_054345167.1XP_054201142.1  chloride channel protein 2 isoform X3

    UniProtKB/TrEMBL
    A0A1B0GUY6