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Aliases for CLCA2 Gene

Aliases for CLCA2 Gene

  • Chloride Channel Accessory 2 2 3
  • Chloride Channel, Calcium Activated, Family Member 2 2 3
  • Calcium-Activated Chloride Channel Family Member 2 3 4
  • Calcium-Activated Chloride Channel Protein 3 3 4
  • Chloride Channel Regulator 2 2 3
  • HCaCC-3 3 4
  • CaCC-3 3 4
  • HCLCA2 3 4
  • CACC3 3 4
  • CLCA Family Member 2, Chloride Channel Regulator 3
  • Calcium-Activated Chloride Channel Regulator 2 3
  • Calcium-Activated Chloride Channel-2 3
  • EC 3.4.-.- 4
  • CLCRG2 3
  • CACC 3

External Ids for CLCA2 Gene

Previous GeneCards Identifiers for CLCA2 Gene

  • GC01P087392
  • GC01P086058
  • GC01P086182
  • GC01P086312
  • GC01P086601
  • GC01P086889
  • GC01P085000

Summaries for CLCA2 Gene

Entrez Gene Summary for CLCA2 Gene

  • The protein encoded by this gene belongs to the calcium sensitive chloride conductance protein family. To date, all members of this gene family map to the same site on chromosome 1p31-p22 and share high degrees of homology in size, sequence and predicted structure, but differ significantly in their tissue distributions. Since this protein is expressed predominantly in trachea and lung, it is suggested to play a role in the complex pathogenesis of cystic fibrosis. It may also serve as adhesion molecule for lung metastatic cancer cells, mediating vascular arrest and colonization, and furthermore, it has been implicated to act as a tumor suppressor gene for breast cancer. [provided by RefSeq, Jul 2008]

GeneCards Summary for CLCA2 Gene

CLCA2 (Chloride Channel Accessory 2) is a Protein Coding gene. Diseases associated with CLCA2 include bestrophinopathy and cystic fibrosis. Among its related pathways are Activation of cAMP-Dependent PKA and Activation of cAMP-Dependent PKA. GO annotations related to this gene include chloride channel activity and ligand-gated ion channel activity. An important paralog of this gene is CLCA1.

UniProtKB/Swiss-Prot for CLCA2 Gene

  • Plays a role in modulating chloride current across the plasma membrane in a calcium-dependent manner, and cell adhesion. Involved in basal cell adhesion and/or stratification of squamous epithelia. May act as a tumor suppressor in breast and colorectal cancer. Plays a key role for cell adhesion in the beginning stages of lung metastasis via the binding to ITGB4.

Tocris Summary for CLCA2 Gene

  • Chloride channels are a family of anion-selective channels involved in a diverse range of biological processes including the regulation of the excitability of neurons, skeletal, cardiac and smooth muscle, cell volume regulation, transepithelial salt transport, the acidification of intra- and extracellular compartments. Ca2+-activated chloride channels (CaCCs) are widely expressed in both excitable and non-excitable cells, are activated by intracellular Ca2+, and modulated by CaMKII and calcineurin.

Gene Wiki entry for CLCA2 Gene

No data available for PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLCA2 Gene

Genomics for CLCA2 Gene

Regulatory Elements for CLCA2 Gene

Genomic Location for CLCA2 Gene

86,424,086 bp from pter
86,456,558 bp from pter
32,473 bases
Plus strand

Genomic View for CLCA2 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for CLCA2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLCA2 Gene

Proteins for CLCA2 Gene

  • Protein details for CLCA2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Calcium-activated chloride channel regulator 2
    Protein Accession:
    Secondary Accessions:
    • A8K2T3
    • Q9Y6N2

    Protein attributes for CLCA2 Gene

    943 amino acids
    Molecular mass:
    103941 Da
    Quaternary structure:
    No Data Available

neXtProt entry for CLCA2 Gene

Proteomics data for CLCA2 Gene at MOPED

Post-translational modifications for CLCA2 Gene

  • N-glycosylated.
  • The 141 kDa mature form is autoproteolytically cleaved by the metalloprotease domain, producing a 109 kDa form and a 35 kDa form. The cleavage is necessary for calcium-activated chloride channel (CaCC) activation activity.
  • Glycosylation at Asn74, Asn150, Asn231, Asn522, and Asn822
  • Modification sites at PhosphoSitePlus

Other Protein References for CLCA2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CLCA2 Gene

Domains for CLCA2 Gene

Protein Domains for CLCA2 Gene

Suggested Antigen Peptide Sequences for CLCA2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Q9UQC9
  • The metalloprotease region is responsible for autoproteolytic processing. It can also cross-cleave other CLCA Substrates.
  • Contains 1 VWFA domain.
  • Belongs to the CLCR family.
genes like me logo Genes that share domains with CLCA2: view

No data available for Gene Families for CLCA2 Gene

Function for CLCA2 Gene

Molecular function for CLCA2 Gene

GENATLAS Biochemistry: chloride channel Ca2+ activated family member 2,outwardly rectifiying,expressed in lung,trachea,mammary gland,epithelial cells
UniProtKB/Swiss-Prot Function: Plays a role in modulating chloride current across the plasma membrane in a calcium-dependent manner, and cell adhesion. Involved in basal cell adhesion and/or stratification of squamous epithelia. May act as a tumor suppressor in breast and colorectal cancer. Plays a key role for cell adhesion in the beginning stages of lung metastasis via the binding to ITGB4.
UniProtKB/Swiss-Prot Induction: Significantly down-regulated in breast and colorectal cancer.

Enzyme Numbers (IUBMB) for CLCA2 Gene

Gene Ontology (GO) - Molecular Function for CLCA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005229 intracellular calcium activated chloride channel activity IBA --
GO:0005254 chloride channel activity TAS 10362588
GO:0008237 metallopeptidase activity IEA --
GO:0015276 ligand-gated ion channel activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with CLCA2: view

Phenotypes for CLCA2 Gene

MGI mutant phenotypes for CLCA2:
inferred from 1 alleles
genes like me logo Genes that share phenotypes with CLCA2: view

Animal Model Products

CRISPR Products

miRNA for CLCA2 Gene

miRTarBase miRNAs that target CLCA2

No data available for Animal Models , Transcription Factor Targeting and HOMER Transcription for CLCA2 Gene

Localization for CLCA2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLCA2 Gene

Cell membrane; Single-pass type I membrane protein. Basal cell membrane; Single-pass type I membrane protein. Cell junction.
Calcium-activated chloride channel regulator 2, 109 kDa form: Secreted. Note=Remains associated to the 35 kDa form until an unidentified event triggers the release.

Subcellular locations from

Jensen Localization Image for CLCA2 Gene COMPARTMENTS Subcellular localization image for CLCA2 gene
Compartment Confidence
extracellular 5
plasma membrane 5
nucleus 1

Gene Ontology (GO) - Cellular Components for CLCA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane TAS 10362588
GO:0009925 basal plasma membrane IEA --
GO:0030054 cell junction IEA --
genes like me logo Genes that share ontologies with CLCA2: view

Pathways for CLCA2 Gene

genes like me logo Genes that share pathways with CLCA2: view

Pathways by source for CLCA2 Gene

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays
    • Lung Cancer in human,mouse,rat

Interacting Proteins for CLCA2 Gene

Gene Ontology (GO) - Biological Process for CLCA2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IEA --
GO:0006810 transport TAS 10362588
GO:0006821 chloride transport --
GO:0007155 cell adhesion IEA --
GO:0034220 ion transmembrane transport TAS --
genes like me logo Genes that share ontologies with CLCA2: view

Compounds for CLCA2 Gene

(5) Tocris Compounds for CLCA2 Gene

Compound Action Cas Number
CaCCinh-A01 Calcium-activated chloride channel (CaCC) inhibitor [407587-33-1]
CFTRinh 172 Voltage-independent, selective CFTR chloride channel blocker [307510-92-5]
Chromanol 293B IKs blocker. Also blocks ICFTR [163163-23-3]
DCPIB Selective blocker of VSAC/ICl, swell. Inhibits glucose-stimulated insulin release [82749-70-0]
Eact Activator of Ca2+-activated Cl- channel transmembrane protein 16A (TMEM16A) [461000-66-8]

(2) HMDB Compounds for CLCA2 Gene

Compound Synonyms Cas Number PubMed IDs
  • Ca
  • Cl2

(1) Novoseek inferred chemical compound relationships for CLCA2 Gene

Compound -log(P) Hits PubMed IDs
chloride 45.4 3
genes like me logo Genes that share compounds with CLCA2: view

Transcripts for CLCA2 Gene

mRNA/cDNA for CLCA2 Gene

Unigene Clusters for CLCA2 Gene

Chloride channel accessory 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CLCA2

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLCA2 Gene

No ASD Table

Relevant External Links for CLCA2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLCA2 Gene

mRNA expression in normal human tissues for CLCA2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLCA2 Gene

This gene is overexpressed in Esophagus - Mucosa (20.3), Vagina (7.9), Skin - Not Sun Exposed (Suprapubic) (7.6), and Skin - Sun Exposed (Lower leg) (6.7).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for CLCA2 Gene

SOURCE GeneReport for Unigene cluster for CLCA2 Gene Hs.241551

mRNA Expression by UniProt/SwissProt for CLCA2 Gene

Tissue specificity: Expressed in cornea, skin, vagina, esophagus, and larynx (at protein level). Expressed in trachea and mammary gland. Weakly expressed in testis and kidney. Highly expressed in corneal epithelium, colon and trachea. Moderately expressed in brain, urogenital organs, bladder, uterus and prostate. Highly expressed in tissues containing stratified epithelium including cornea, esophagus, larynx, skin and vagina than those tissues which contain only epithelial monolayers. Expressed in normal breast epithelium but not in breast cancer. Highly expressed during epithelial stratification. Expressed in endothelial cells of lung. Expressed selectively in endothelia of small pulmonary arteries, arterioles, and subpleural and interlobular venules.
genes like me logo Genes that share expressions with CLCA2: view

In Situ Assay Products

Orthologs for CLCA2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLCA2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CLCA2 35
  • 99.43 (n)
  • 98.94 (a)
CLCA2 36
  • 99 (a)
(Bos Taurus)
Mammalia CLCA2 35
  • 87.5 (n)
  • 83.48 (a)
CLCA2 36
  • 84 (a)
(Canis familiaris)
Mammalia CLCA2 35
  • 88.87 (n)
  • 84.84 (a)
CLCA2 36
  • 85 (a)
(Mus musculus)
Mammalia Clca5 35
  • 78.84 (n)
  • 72.19 (a)
Clca5 16
Clca5 36
  • 72 (a)
(Monodelphis domestica)
Mammalia CLCA2 36
  • 64 (a)
(Ornithorhynchus anatinus)
Mammalia CLCA2 36
  • 63 (a)
(Rattus norvegicus)
Mammalia Clca5 35
  • 79.36 (n)
  • 73.69 (a)
(Gallus gallus)
Aves CLCA2 35
  • 61.99 (n)
  • 52.28 (a)
CLCA2 36
  • 51 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.15133 35
(Danio rerio)
Actinopterygii si:ch211-116o3.3 36
  • 46 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 28 (a)
-- 36
  • 32 (a)
-- 36
  • 24 (a)
-- 36
  • 37 (a)
-- 36
  • 27 (a)
Species with no ortholog for CLCA2:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • 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 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)
  • worm (Caenorhabditis elegans)

Evolution for CLCA2 Gene

Gene Tree for CLCA2 (if available)
Gene Tree for CLCA2 (if available)

Paralogs for CLCA2 Gene

Paralogs for CLCA2 Gene

Selected SIMAP similar genes for CLCA2 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with CLCA2: view

Variants for CLCA2 Gene

Sequence variations from dbSNP and Humsavar for CLCA2 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs16908 -- 86,437,124(+) TCATC(C/T)GAAAT intron-variant
rs883200 -- 86,422,815(+) CCTTG(C/G)TGGGA upstream-variant-2KB
rs956499 -- 86,438,508(+) TGCAA(A/T)GTTTT intron-variant
rs969786 -- 86,451,084(+) AAAGA(A/G)GCAAA intron-variant
rs969787 -- 86,451,138(+) TCCAC(A/G)CAAGA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CLCA2 Gene

Variant ID Type Subtype PubMed ID
nsv871081 CNV Loss 21882294
nsv521366 CNV Loss 19592680

Relevant External Links for CLCA2 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLCA2 Gene

Disorders for CLCA2 Gene

MalaCards: The human disease database

MalaCards: The human disease database. (3) Diseases for CLCA2 Gene including...

Search for CLCA2 Gene in MalaCards »

(2) University of Copenhagen DISEASES for CLCA2 Gene

Relevant External Links for CLCA2

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with CLCA2: view

No data available for UniProtKB/Swiss-Prot for CLCA2 Gene

Publications for CLCA2 Gene

  1. Identification of three novel members of the calcium-dependent chloride channel (CaCC) family predominantly expressed in the digestive tract and trachea. (PMID: 10437792) Agnel M. … Culouscou J.-M. (FEBS Lett. 1999) 3 4 23
  2. The quantification of hCLCA2 and colocalisation with integrin beta4 in stratified human epithelia. (PMID: 15707651) Connon C.J. … Kinoshita S. (Acta Histochem. 2005) 3 4 23
  3. Modulation of Ca2+-activated Cl- secretion by basolateral K+ channels in human normal and cystic fibrosis airway epithelia. (PMID: 12612194) Mall M. … Kunzelmann K. (Pediatr. Res. 2003) 3 23
  4. Molecular cloning and transmembrane structure of hCLCA2 from human lung, trachea, and mammary gland. (PMID: 10362588) Gruber A.D. … Pauli B.U. (Am. J. Physiol. 1999) 3 4
  5. Tumorigenicity of human breast cancer is associated with loss of the Ca2+-activated chloride channel CLCA2. (PMID: 10554024) Gruber A.D. … Pauli B.U. (Cancer Res. 1999) 3 4

Products for CLCA2 Gene

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