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Aliases for CLCN2 Gene

Aliases for CLCN2 Gene

  • Chloride Channel, Voltage-Sensitive 2 2 3
  • Chloride Channel 2 2 3
  • ClC-2 3 4
  • EGI11 3 6
  • LKPAT 3 6
  • ECA2 3 6
  • EGMA 3 6
  • EJM8 3 6
  • Chloride Channel Protein 2 3
  • CIC-2 3
  • EJM6 3
  • CLC2 3
  • ECA3 3
  • EGI3 3

External Ids for CLCN2 Gene

Previous GeneCards Identifiers for CLCN2 Gene

  • GC03P180523
  • GC03M185057
  • GC03M185466
  • GC03M185385
  • GC03M185546
  • GC03M184063
  • GC03M181470

Summaries for CLCN2 Gene

Entrez Gene Summary for CLCN2 Gene

  • 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]

GeneCards Summary for CLCN2 Gene

CLCN2 (Chloride Channel, Voltage-Sensitive 2) is a Protein Coding gene. Diseases associated with CLCN2 include epilepsy, idiopathic generalized 11 and leukoencephalopathy with ataxia. Among its related pathways are Activation of cAMP-Dependent PKA and Activation of cAMP-Dependent PKA. GO annotations related to this gene include voltage-gated chloride channel activity and adenyl nucleotide binding. An important paralog of this gene is CLCN7.

UniProtKB/Swiss-Prot for CLCN2 Gene

  • Voltage-gated chloride channel. Chloride channels have several functions including the regulation of cell volume; membrane potential stabilization, signal transduction and transepithelial transport.

Gene Wiki entry for CLCN2 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLCN2 Gene

Genomics for CLCN2 Gene

Regulatory Elements for CLCN2 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for CLCN2 Gene

184,346,185 bp from pter
184,361,651 bp from pter
15,467 bases
Minus strand

Genomic View for CLCN2 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for CLCN2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLCN2 Gene

Proteins for CLCN2 Gene

  • Protein details for CLCN2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Chloride channel protein 2
    Protein Accession:
    Secondary Accessions:
    • B4DQT9
    • B4DZ58
    • E9PBD9
    • E9PCD2
    • O14864
    • Q6IPA9
    • Q8WU13

    Protein attributes for CLCN2 Gene

    898 amino acids
    Molecular mass:
    98535 Da
    Quaternary structure:
    No Data Available
    • The CLC channel family contains both chloride channels and proton-coupled anion transporters that exchange chloride or another anion for protons. The absence of conserved gating glutamate residues is typical for family members that function as channels (By similarity).
    • Sequence=AAH21578.1; Type=Erroneous translation; Note=Wrong choice of frame.; Evidence={ECO:0000305};

    Alternative splice isoforms for CLCN2 Gene


neXtProt entry for CLCN2 Gene

Proteomics data for CLCN2 Gene at MOPED

Post-translational modifications for CLCN2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CLCN2 Gene

No data available for DME Specific Peptides for CLCN2 Gene

Domains for CLCN2 Gene

Gene Families for CLCN2 Gene

  • CLCN :Ion channels / Chloride channels : Voltage-sensitive

Suggested Antigen Peptide Sequences for CLCN2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • P51788
  • Contains 2 CBS domains.
  • Belongs to the chloride channel (TC 2.A.49) family. ClC-2/CLCN2 subfamily.
genes like me logo Genes that share domains with CLCN2: view

Function for CLCN2 Gene

Molecular function for CLCN2 Gene

GENATLAS Biochemistry: chloride voltage-gated channel 2,widely expressed
UniProtKB/Swiss-Prot Function: Voltage-gated chloride channel. Chloride channels have several functions including the regulation of cell volume; membrane potential stabilization, signal transduction and transepithelial transport.

Gene Ontology (GO) - Molecular Function for CLCN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005216 ion channel activity --
GO:0005247 voltage-gated chloride channel activity IEA --
GO:0030554 adenyl nucleotide binding --
genes like me logo Genes that share ontologies with CLCN2: view
genes like me logo Genes that share phenotypes with CLCN2: view

Animal Models for CLCN2 Gene

MGI Knock Outs for CLCN2:

Animal Model Products

CRISPR Products

miRNA for CLCN2 Gene

miRTarBase miRNAs that target CLCN2

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for CLCN2 Gene

Localization for CLCN2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLCN2 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

Jensen Localization Image for CLCN2 Gene COMPARTMENTS Subcellular localization image for CLCN2 gene
Compartment Confidence
plasma membrane 4
peroxisome 1

Gene Ontology (GO) - Cellular Components for CLCN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0016020 membrane --
GO:0034707 chloride channel complex IEA --
genes like me logo Genes that share ontologies with CLCN2: view

Pathways for CLCN2 Gene

genes like me logo Genes that share pathways with CLCN2: view

Pathways by source for CLCN2 Gene

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Interacting Proteins for CLCN2 Gene

Gene Ontology (GO) - Biological Process for CLCN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport TAS 7795595
GO:0006821 chloride transport --
GO:0034220 ion transmembrane transport TAS --
GO:0034765 regulation of ion transmembrane transport --
GO:0044070 regulation of anion transport --
genes like me logo Genes that share ontologies with CLCN2: view

Compounds for CLCN2 Gene

(1) HMDB Compounds for CLCN2 Gene

Compound Synonyms Cas Number PubMed IDs
  • Cl2

(1) Drugbank Compounds for CLCN2 Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
136790-76-6 target inducer

(8) IUPHAR Ligand for CLCN2 Gene

Ligand Type Action Affinity Pubmed IDs
GaTx2 Channel blocker None 10.8
NPPB Activator Activation 6.49
Zn2+ Channel blocker None 6
omeprazole Activator None
Cd2+ Channel blocker None
lubiprostone Activator None
DPC Channel blocker None
arachidonic acid Activator Potentiation

(6) Novoseek inferred chemical compound relationships for CLCN2 Gene

Compound -log(P) Hits PubMed IDs
lubiprostone 95.8 10
chloride 84.5 47
halide 52.3 1
atp 0 4
sodium 0 1
genes like me logo Genes that share compounds with CLCN2: view

Transcripts for CLCN2 Gene

Unigene Clusters for CLCN2 Gene

Chloride channel, voltage-sensitive 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CLCN2

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for CLCN2

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLCN2 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17a · 17b ^ 18 ^ 19 ^ 20a · 20b ^ 21 ^ 22 ^
SP1: - -
SP2: - -

ExUns: 23 ^ 24

Relevant External Links for CLCN2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLCN2 Gene

mRNA expression in normal human tissues for CLCN2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLCN2 Gene

This gene is overexpressed in Nerve - Tibial (4.7).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for CLCN2 Gene

SOURCE GeneReport for Unigene cluster for CLCN2 Gene Hs.436847

mRNA Expression by UniProt/SwissProt for CLCN2 Gene

Tissue specificity: Ubiquitously expressed. Moderately expressed in aortic and coronary vascular smooth muscle cells and expressed at a low level in aortic endothelial cells.
genes like me logo Genes that share expressions with CLCN2: view

In Situ Assay Products

Orthologs for CLCN2 Gene

This gene was present in the common ancestor of animals.

Orthologs for CLCN2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CLCN2 35
  • 99.62 (n)
  • 99.54 (a)
CLCN2 36
  • 100 (a)
(Bos Taurus)
Mammalia CLCN2 35
  • 90.14 (n)
  • 94.71 (a)
CLCN2 36
  • 93 (a)
(Canis familiaris)
Mammalia CLCN2 35
  • 91.28 (n)
  • 95.6 (a)
CLCN2 36
  • 95 (a)
(Mus musculus)
Mammalia Clcn2 35
  • 88.09 (n)
  • 94.49 (a)
Clcn2 16
Clcn2 36
  • 93 (a)
(Monodelphis domestica)
Mammalia CLCN2 36
  • 88 (a)
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 96 (a)
-- 36
  • 78 (a)
(Rattus norvegicus)
Mammalia Clcn2 35
  • 88.28 (n)
  • 94.38 (a)
(Gallus gallus)
Aves CLCN2 35
  • 75.12 (n)
  • 77.37 (a)
CLCN2 36
  • 76 (a)
(Anolis carolinensis)
Reptilia -- 36
  • 76 (a)
-- 36
  • 84 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia clcn2 35
  • 69.43 (n)
  • 77.22 (a)
(Danio rerio)
Actinopterygii CLCN2 36
  • 72 (a)
LOC100333644 35
  • 70.35 (n)
  • 73.73 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta GPRMGL4 35
  • 57.33 (n)
  • 52.95 (a)
fruit fly
(Drosophila melanogaster)
Insecta ClC-a 35
  • 55.94 (n)
  • 52.8 (a)
ClC-a 36
  • 37 (a)
(Caenorhabditis elegans)
Secernentea clh-1 36
  • 32 (a)
clh-2 36
  • 34 (a)
clh-3 35
  • 49.54 (n)
  • 46.8 (a)
clh-3 36
  • 35 (a)
clh-4 36
  • 28 (a)
clh-3 37
  • 42 (a)
Species with no ortholog for CLCN2:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CLCN2 Gene

Gene Tree for CLCN2 (if available)
Gene Tree for CLCN2 (if available)

Paralogs for CLCN2 Gene

Paralogs for CLCN2 Gene

Selected SIMAP similar genes for CLCN2 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with CLCN2: view

Variants for CLCN2 Gene

Sequence variations from dbSNP and Humsavar for CLCN2 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type MAF
rs2228291 -- 184,357,259(-) ACTAT(C/T)ACAGC synonymous-codon, reference, upstream-variant-2KB
rs2228292 - 184,352,800(-) GCAGA(C/G)TCGGC missense, reference
rs2293603 -- 184,347,128(-) ATCTG(G/T)GGCAC intron-variant
rs3749221 -- 184,355,763(-) TTCCC(A/G)GCTCT synonymous-codon, reference, utr-variant-5-prime
rs3749222 -- 184,354,844(-) CCCCC(C/G)CAGCC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CLCN2 Gene

Variant ID Type Subtype PubMed ID
nsv878057 CNV Loss 21882294
nsv878060 CNV Loss 21882294
nsv829813 CNV Loss 17160897
esv2422400 CNV Duplication 17116639

Relevant External Links for CLCN2 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLCN2 Gene

Disorders for CLCN2 Gene

(2) OMIM Diseases for CLCN2 Gene (600570)


  • Epilepsy, idiopathic generalized 11 (EIG11) [MIM:607628]: A disorder characterized by recurring generalized seizures in the absence of detectable brain lesions and/or metabolic abnormalities. Generalized seizures arise diffusely and simultaneously from both hemispheres of the brain. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
  • Juvenile absence epilepsy 2 (JAE2) [MIM:607628]: A subtype of idiopathic generalized epilepsy characterized by onset occurring around puberty, absence seizures, generalized tonic-clonic seizures (GTCS), GTCS on awakening, and myoclonic seizures. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
  • Juvenile myoclonic epilepsy 8 (EJM8) [MIM:607628]: A subtype of idiopathic generalized epilepsy. Patients have afebrile seizures only, with onset in adolescence (rather than in childhood) and myoclonic jerks which usually occur after awakening and are triggered by sleep deprivation and fatigue. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
  • Leukoencephalopathy with ataxia (LKPAT) [MIM:615651]: An autosomal recessive neurologic disorder with a characteristic pattern of white matter abnormalities on brain MRI. Affected individuals have prominent signal abnormalities and decreased apparent diffusion coefficient values in the posterior limbs of the internal capsules, middle cerebral peduncles, pyramidal tracts in the pons, and middle cerebellar peduncles, suggesting myelin microvacuolation. Clinical features include ataxia and unstable gait. More variable abnormalities may include visual field defects, headaches, and learning disabilities. {ECO:0000269 PubMed:23707145}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(2) University of Copenhagen DISEASES for CLCN2 Gene

(5) Novoseek inferred disease relationships for CLCN2 Gene

Disease -log(P) Hits PubMed IDs
cystic fibrosis 57.8 6
malignant glioma 25.1 2
epilepsy 20.2 4
shock 5.99 3
glioma 1.95 5

Relevant External Links for CLCN2

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with CLCN2: view

Publications for CLCN2 Gene

  1. Two novel CLCN2 mutations accelerating chloride channel deactivation are associated with idiopathic generalized epilepsy. (PMID: 19191339) Saint-Martin C. … Depienne C. (Hum. Mutat. 2009) 3 4 23 48
  2. Cloning of a putative human voltage-gated chloride channel (ClC-2) cDNA widely expressed in human tissues. (PMID: 7795595) Cid L.P. … Cutting G.R. (Hum. Mol. Genet. 1995) 2 3 4
  3. CLC-2 single nucleotide polymorphisms (SNPs) as potential modifiers of cystic fibrosis disease severity. (PMID: 15507145) Blaisdell C.J. … Stine O.C. (BMC Med. Genet. 2004) 3 23 48
  4. Alterations in the cytoplasmic domain of CLCN2 result in altered gating kinetics. (PMID: 17762171) Paul J. … Kun J.F.J. (Cell. Physiol. Biochem. 2007) 3 4 23
  5. Expression of CLCN voltage-gated chloride channel genes in human blood vessels. (PMID: 10198195) Lamb F.S. … Schutte B.C. (J. Mol. Cell. Cardiol. 1999) 3 4 23

Products for CLCN2 Gene

Sources for CLCN2 Gene

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