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Aliases for CLCN2 Gene

Aliases for CLCN2 Gene

  • Chloride Voltage-Gated Channel 2 2 3 5
  • Chloride Channel, Voltage-Sensitive 2 2 3
  • Chloride Channel 2 2 3
  • ClC-2 3 4
  • Chloride Channel Protein 2 3
  • CIC-2 3
  • EGI11 3
  • LKPAT 3
  • EJM6 3
  • CLC2 3
  • ECA2 3
  • ECA3 3
  • EGI3 3
  • EGMA 3
  • EJM8 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 Voltage-Gated Channel 2) is a Protein Coding gene. Diseases associated with CLCN2 include Leukoencephalopathy With Ataxia and Epilepsy, Idiopathic Generalized 11. Among its related pathways are Ion channel transport and Hepatic ABC Transporters. GO annotations related to this gene include ion channel activity and voltage-gated chloride channel activity. An important paralog of this gene is CLCN1.

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

Enhancers for CLCN2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03F184523 1.3 Ensembl ENCODE 11.3 -163.6 -163551 2.8 PKNOX1 ARID4B SIN3A DMAP1 ZNF48 GLIS2 FOS PAF1 SP3 SP5 MAGEF1 LINC02054 CHRD THPO LINC01840 CLCN2 POLR2H EPHB3 FAM131A EIF4G1
GH03F184417 0.9 ENCODE 10.8 -56.4 -56377 0.2 ATF1 ZNF76 SIN3A ARID4B ZNF48 RAD21 ZNF121 GLIS2 ZNF143 THAP11 CHRD THPO LINC01840 EPHB3 FAM131A POLR2H CLCN2 EIF4G1 PSMD2 LINC02054
GH03F184354 0.7 ENCODE 0.4 +7.2 7194 0.1 HDGF CTCF MAZ ZNF740 REST ZBTB7A RAD21 ZFHX2 GLIS2 EGR1 GC03M184355 PIR35526 CLCN2
GH03F184359 0.2 Ensembl 0.8 +2.0 1951 0.2 KLHL24 CLCN2 GC03M184355 PIR35526
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CLCN2 on UCSC Golden Path with GeneCards custom track

Promoters for CLCN2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001855685 1151 201 HIC1 ZNF366 ZNF512 USF2

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

Genes around CLCN2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLCN2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

Post-translational modifications for CLCN2 Gene

Antibody Products

  • Abcam antibodies for CLCN2

No data available for DME Specific Peptides for CLCN2 Gene

Domains & Families for CLCN2 Gene

Gene Families for CLCN2 Gene

Suggested Antigen Peptide Sequences for CLCN2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 2 CBS domains.
  • Belongs to the chloride channel (TC 2.A.49) family. ClC-2/CLCN2 subfamily.
  • 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:0005244 voltage-gated ion channel activity IEA --
GO:0005247 voltage-gated chloride channel activity IEA,TAS --
GO:0005254 chloride channel activity IEA --
GO:0031404 chloride ion binding IBA --
genes like me logo Genes that share ontologies with CLCN2: view
genes like me logo Genes that share phenotypes with CLCN2: view

Human Phenotype Ontology for CLCN2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CLCN2 Gene

MGI Knock Outs for CLCN2:

Animal Model Products

miRNA for CLCN2 Gene

miRTarBase miRNAs that target CLCN2

Flow Cytometry Products

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

Localization for CLCN2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLCN2 Gene

Cell membrane; Multi-pass membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLCN2 gene
Compartment Confidence
plasma membrane 5
extracellular 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for CLCN2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0034707 chloride channel complex IEA --
genes like me logo Genes that share ontologies with CLCN2: view

Pathways & Interactions for CLCN2 Gene

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

Pathways by source 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:0006811 ion transport IEA --
GO:0006821 chloride transport IEA --
GO:0034220 ion transmembrane transport IEA,TAS --
GO:0034765 regulation of ion transmembrane transport IEA --
genes like me logo Genes that share ontologies with CLCN2: view

No data available for SIGNOR curated interactions for CLCN2 Gene

Drugs & Compounds for CLCN2 Gene

(11) Drugs for CLCN2 Gene - From: DrugBank, ApexBio, DGIdb, IUPHAR, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Lubiprostone Approved, Investigational Pharma Activator, activator, Target, inducer 45
Omeprazole Approved, Investigational, Vet_approved Pharma Activator, inhibitor H+,K+-ATPase inhibitor 337
arachidonic acid Experimental Nutra Activator 28
GaTx2 Pharma Channel blocker 0
NPPB Pharma Channel blocker inhibitor of chloride channel 0

(6) Additional Compounds for CLCN2 Gene - From: Novoseek, IUPHAR, and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Channel blocker
Chloride ion
  • Bertholite
  • Chloor
  • Chlor
  • Chlore
  • Chloride

(4) ApexBio Compounds for CLCN2 Gene

Compound Action Cas Number
9-AC 723-62-6
DCPIB 82749-70-0
GaTx2 194665-85-5
NPPB inhibitor of chloride channel 107254-86-4
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:

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 from GTEx, Illumina, BioGPS, and SAGE 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 (x4.7).

Protein differential expression in normal tissues from HIPED for CLCN2 Gene

This gene is overexpressed in Testis (57.4) and Spinal cord (11.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CLCN2 Gene

Protein tissue co-expression partners for CLCN2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CLCN2 Gene:


SOURCE GeneReport for Unigene cluster for CLCN2 Gene:


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 expression patterns with CLCN2: view

Primer 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 34 35
  • 99.62 (n)
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 96 (a)
-- 35
  • 78 (a)
(Canis familiaris)
Mammalia CLCN2 34 35
  • 91.28 (n)
(Bos Taurus)
Mammalia CLCN2 34 35
  • 90.14 (n)
(Rattus norvegicus)
Mammalia Clcn2 34
  • 88.28 (n)
(Mus musculus)
Mammalia Clcn2 34 16 35
  • 88.09 (n)
(Monodelphis domestica)
Mammalia CLCN2 35
  • 88 (a)
(Gallus gallus)
Aves CLCN2 34 35
  • 75.12 (n)
(Anolis carolinensis)
Reptilia -- 35
  • 84 (a)
-- 35
  • 76 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia clcn2 34
  • 69.43 (n)
(Danio rerio)
Actinopterygii CLCN2 35
  • 72 (a)
LOC100333644 34
  • 70.35 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta GPRMGL4 34
  • 57.33 (n)
fruit fly
(Drosophila melanogaster)
Insecta ClC-a 34 35
  • 55.94 (n)
(Caenorhabditis elegans)
Secernentea clh-3 36 34 35
  • 49.54 (n)
clh-2 35
  • 34 (a)
clh-1 35
  • 32 (a)
clh-4 35
  • 28 (a)
Species where no ortholog for CLCN2 was found in the sources mined by GeneCards:
  • 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

(3) 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
rs137852682 Epilepsy, idiopathic generalized 11 (EIG11) [MIM:607628], other 184,353,787(-) GTACC(A/G)GGTGC nc-transcript-variant, reference, missense
rs587777111 Leukoencephalopathy with ataxia (LKPAT) [MIM:615651], Pathogenic 184,354,556(+) CCACA(A/G/T)CGTAG nc-transcript-variant, reference, missense
rs71318369 Juvenile myoclonic epilepsy 8 (EJM8) [MIM:607628], other 184,357,688(+) TGTTC(C/T)GGGAT intron-variant, nc-transcript-variant, reference, missense
rs141242566 Pathogenic 184,353,722(+) CAGGT(A/C/T)CCGGA nc-transcript-variant, reference, missense
rs201330912 Pathogenic 184,354,113(+) GGCCC(C/T)AGCCG nc-transcript-variant, reference, stop-gained

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

Variant ID Type Subtype PubMed ID
esv2422400 CNV duplication 17116639
nsv829813 CNV loss 17160897

Variation tolerance for CLCN2 Gene

Residual Variation Intolerance Score: 43.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.82; 93.42% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CLCN2 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

Disorders for CLCN2 Gene

MalaCards: The human disease database

(16) MalaCards diseases for CLCN2 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
leukoencephalopathy with ataxia
  • lkpat
epilepsy, idiopathic generalized 11
  • epilepsy, juvenile myoclonic 8
leukoencephalopathy with ataxia due to clc-2 deficiency
  • leukoencephalopathy with ataxia
clcn2-related juvenile myoclonic epilepsy
juvenile absence epilepsy
  • childhood absence epilepsy
- elite association - COSMIC cancer census association via MalaCards
Search CLCN2 in MalaCards View complete list of genes associated with diseases


  • 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. {ECO:0000269 PubMed:19191339}. 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. {ECO:0000269 PubMed:12612585, ECO:0000269 PubMed:19710712}. Note=Disease susceptibility may be 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. {ECO:0000269 PubMed:19191339}. 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.

Relevant External Links for CLCN2

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with CLCN2: view

No data available for Genatlas for CLCN2 Gene

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 22 46 64
  2. 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 22 64
  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 22 46 64
  4. 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 22 64
  5. 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 64

Products for CLCN2 Gene

Sources for CLCN2 Gene

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