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CLCA2 Gene

protein-coding   GIFtS: 63
GCID: GC01P086889

Chloride Channel Accessory 2

(Previous names: chloride channel, calcium activated, family member 2, chloride...)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Chloride Channel Accessory 21 2     hCLCA22 3
Chloride Channel Regulator 21 2     hCaCC-32 3
Chloride Channel, Calcium Activated, Family Member 21 2     CACC2
Calcium-Activated Chloride Channel Family Member 22 3     CLCRG22
Calcium-Activated Chloride Channel Protein 32 3     Calcium-Activated Chloride Channel Regulator 22
CACC32 3     Calcium-Activated Chloride Channel-22
CaCC-32 3     CLCA Family Member 2, Chloride Channel Regulator2

External Ids:    HGNC: 20161   Entrez Gene: 96352   Ensembl: ENSG000001379757   OMIM: 6040035   UniProtKB: Q9UQC93   

Export aliases for CLCA2 gene to outside databases

Previous GC identifers: GC01P087392 GC01P086058 GC01P086182 GC01P086312 GC01P086601 GC01P085000


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 breast and colorectal cancer. GO annotations related to this gene include chloride channel activity and ligand-gated ion channel activity. An important paralog of this gene is CLCA4.

UniProtKB/Swiss-Prot: CLCA2_HUMAN, Q9UQC9
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

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


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000001.11  NC_018912.2  NT_032977.10  
Regulatory elements:
   Regulatory transcription factor binding sites in the CLCA2 gene promoter:
         GR   Pbx1a   GR-beta   FOXD3   Tal-1beta   FOXJ2 (long isoform)   ZID   GR-alpha   ITF-2   TGIF   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCLCA2 promoter sequence
   Search Chromatin IP Primers for CLCA2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CLCA2


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1p22.3   Ensembl cytogenetic band:  1p22.3   HGNC cytogenetic band: 1p22.3

CLCA2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLCA2 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01P086889:  view genomic region     (about GC identifiers)

Start:
86,889,769 bp from pter      End:
86,922,241 bp from pter
Size:
32,473 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: CLCA2_HUMAN, Q9UQC9 (See protein sequence)
Recommended Name: Calcium-activated chloride channel regulator 2 precursor  
Size: 943 amino acids; 103941 Da
Secondary accessions: A8K2T3 Q9Y6N2

Explore the universe of human proteins at neXtProt for CLCA2: NX_Q9UQC9

Explore proteomics data for CLCA2 at MOPED

Post-translational modifications: 

  • The 141 kDa mature form is shedded, producing a 109 kDa form and a 35 kDa form1
  • N-glycosylated1
  • Glycosylation2 at Asn74, Asn150, Asn231, Asn522, Asn822
  • Modification sites at PhosphoSitePlus

  • See CLCA2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_006527.1  
    ENSEMBL proteins: 
     ENSP00000359596  

    CLCA2 Human Recombinant Protein Products:

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    Novus Biologicals CLCA2 Protein
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    Cloud-Clone Corp. Proteins for CLCA2

    CLCA2 Antibody Products:

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    LSBio Antibodies in human, mouse, rat for CLCA2

    CLCA2 Assay Products:

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    Cloud-Clone Corp. ELISAs for CLCA2
    Cloud-Clone Corp. CLIAs for CLCA2


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    4 InterPro protein domains:
     IPR013642 Cl_channel_Ca
     IPR004727 CaCC_prot
     IPR015394 DUF1973
     IPR002035 VWF_A

    Graphical View of Domain Structure for InterPro Entry Q9UQC9

    ProtoNet protein and cluster: Q9UQC9

    UniProtKB/Swiss-Prot: CLCA2_HUMAN, Q9UQC9
    Similarity: Belongs to the CLCR family
    Similarity: Contains 1 VWFA domain


    CLCA2 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CLCA2_HUMAN, Q9UQC9
    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
    Induction: Significantly down-regulated in breast and colorectal cancer

         Genatlas biochemistry entry for CLCA2:
    chloride channel Ca2+ activated family member 2,outwardly rectifiying,expressed in lung,trachea,mammary
    gland,epithelial cells

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005254chloride channel activity IEA--
    GO:0015276ligand-gated ion channel activity IEA--
         
    CLCA2 for ontologies           About GeneDecksing


    Phenotypes:
         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Clca5):
     liver/biliary system 

    CLCA2 for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for CLCA2
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for CLCA2

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for CLCA2
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for CLCA2

    miRNA
    Products:
        
    miRTarBase miRNAs that target CLCA2:
    hsa-let-7b-5p (MIRT051890)

    Block miRNA regulation of human, mouse, rat CLCA2 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate CLCA2 (see all 15):
    hsa-miR-3163 hsa-miR-548w hsa-miR-548j hsa-miR-559 hsa-miR-548h hsa-miR-548i hsa-miR-548c-5p hsa-miR-548y
    SwitchGear 3'UTR luciferase reporter plasmidCLCA2 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for CLCA2
    Predesigned siRNA for gene silencing in human, mouse, rat CLCA2

    Gene Editing
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    DNA2.0 Custom Protein Engineering Service for CLCA2

    Clone
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    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: CLCA2 (NM_006536)
    Sino Biological Human cDNA Clone for CLCA2
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for CLCA2
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CLCA2

    Cell Line
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    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLCA2


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    CLCA2_HUMAN, Q9UQC9: Cell membrane; Single-pass type I membrane protein. Basal cell membrane; Single-pass type I
    membrane protein. Cell junction
    CLCA2_HUMAN, Q9UQC9: 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 COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    plasma membrane5
    nucleus1

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--
    GO:0005886plasma membrane ----
    GO:0005887integral component of plasma membrane TAS10362588
    GO:0009925basal plasma membrane IEA--
    GO:0030054cell junction IEA--

    CLCA2 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for CLCA2 About   (see all 7)                                                                                              See pathways by source

    SuperPathContained pathways About
    1Activation of cAMP-Dependent PKA
    Activation of cAMP-Dependent PKA0.77
    PKA Signaling0.56
    cAMP Pathway0.77
    2Olfactory Signaling Pathway
    Olfactory transduction0.82
    3Hepatic ABC Transporters
    Hepatic ABC Transporters0.41
    4Neuropathic Pain-Signaling in Dorsal Horn Neurons
    Cholera Infection0.40
    5Pancreatic secretion
    Pancreatic secretion

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    5 Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for CLCA2
        Cholera Infection
    Hepatic ABC Transporters
    PKA Signaling
    cAMP Pathway
    Activation of cAMP-Dependent PKA

    1 GeneGo (Thomson Reuters) Pathway for CLCA2
        CFTR-dependent regulation of ion channels in Airway Epithelium (norm and CF)

    1 BioSystems Pathway for CLCA2
        Alpha6-Beta4 Integrin Signaling Pathway



    2 Kegg Pathways  (Kegg details for CLCA2):
        Olfactory transduction
    Pancreatic secretion


    CLCA2 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Array including CLCA2: 
              Lung Cancer in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for CLCA2

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    4 Interacting proteins for CLCA2 (Q9UQC93 ENSP000003595964) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ITGB4P161443, ENSP000002001814I2D: score=1 STRING: ENSP00000200181
    ALBP027683, ENSP000002958974I2D: score=1 STRING: ENSP00000295897
    CNGA3ENSP000002726024STRING: ENSP00000272602
    CNGA4ENSP000003692684STRING: ENSP00000369268
    About this table

    Gene Ontology (GO): 4 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006810transport TAS10362588
    GO:0006821chloride transport ----
    GO:0007155cell adhesion IEA--
    GO:1902476chloride transmembrane transport TAS10362588

    CLCA2 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Compounds for CLCA2 available from Tocris Bioscience    About this table
    CompoundAction CAS #
    DCPIB Selective blocker of VSAC/ICl, swell. Inhibits glucose-stimulated insulin release [82749-70-0]
    Chromanol 293BIKs blocker. Also blocks ICFTR[163163-23-3]
    NPPBInhibits calcium-sensitive chloride currents[107254-86-4]
    LonidamineMitochondrial hexokinase inhibitor[50264-69-2]
    CFTRinh 172 Voltage-independent, selective CFTR chloride channel blocker [307510-92-5]

    2 HMDB Compounds for CLCA2    About this table
    CompoundSynonyms CAS #PubMed Ids
    CalciumCa (see all 2)7440-70-2--
    ChlorineCl2 (see all 13)16887-00-6--

    1 Novoseek inferred chemical compound relationship for CLCA2 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    chloride 45.4 3 10437792 (2), 15707651 (1)



    CLCA2 for compounds           About GeneDecksing



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for CLCA2 gene: 
    NM_006536.5  

    Unigene Cluster for CLCA2:

    Chloride channel accessory 2
    Hs.241551  [show with all ESTs]
    Unigene Representative Sequence: NM_006536
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000370565(uc001dlr.4) ENST00000490884 ENST00000498802
    miRNA
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    Block miRNA regulation of human, mouse, rat CLCA2 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate CLCA2 (see all 15):
    hsa-miR-3163 hsa-miR-548w hsa-miR-548j hsa-miR-559 hsa-miR-548h hsa-miR-548i hsa-miR-548c-5p hsa-miR-548y
    SwitchGear 3'UTR luciferase reporter plasmidCLCA2 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for CLCA2
    Predesigned siRNA for gene silencing in human, mouse, rat CLCA2
    Clone
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    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: CLCA2 (NM_006536)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CLCA2
    Primer
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat CLCA2
      QuantiTect SYBR Green Assays in human, mouse, rat CLCA2
      QuantiFast Probe-based Assays in human, mouse, rat CLCA2

    Additional mRNA sequence: 

    AB026833.1 AF043977.1 AF127980.1 AK290348.1 AK296719.1 AK307937.1 BC041096.1 

    4 DOTS entries:

    DT.435997  DT.40115271  DT.106056  DT.92466956 

    Selected AceView cDNA sequences (see all 56):

    BG696011 AL602490 AA443258 AA446075 BP351722 AA687942 BC041096 BG695888 
    BX504441 AL598508 AF127980 AW173757 BG678906 AA430264 NM_006536 BP351753 
    BG675746 BX505072 BM921268 BX476731 BX505224 AI493356 BG742015 AI830842 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    CLCA2 expression in normal human tissues (normalized intensities)      CLCA2 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AAAGCCACAG
    CLCA2 Expression
    About this image


    CLCA2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 7) fully expand
     
     Esophagus (Gastrointestinal Tract)    fully expand to see all 3 entries
             esophagus ; squamous epithelial cells   
             esophageal epithelium   
     
     Epithelial Cells (Uncategorized)    fully expand to see all 3 entries
             esophagus ; squamous epithelial cells   
             esophageal epithelium   
     
     Lung (Respiratory System)
             Basal Cells Trachea
     
     Pancreas (Endocrine System)
             Islets of Langerhans
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
    CLCA2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CLCA2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.241551

    UniProtKB/Swiss-Prot: CLCA2_HUMAN, Q9UQC9
    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

        Pathway & Disease-focused RT2 Profiler PCR Array including CLCA2: 
              Lung Cancer in human mouse rat

    Primer
    Products:
    OriGene qPCR primer pairs and template standards for CLCA2
    OriGene qSTAR qPCR primer pairs in human, mouse for CLCA2
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat CLCA2
    QuantiTect SYBR Green Assays in human, mouse, rat CLCA2
    QuantiFast Probe-based Assays in human, mouse, rat CLCA2
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLCA2

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for CLCA2 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Clca51 , 5 chloride channel calcium activated 51, 5 78.84(n)1
    72.19(a)1
      3 (69.31 cM)5
    2299331  NM_178697.41  NP_848812.11 
     1450702655 
    chicken
    (Gallus gallus)
    Aves CLCA21 chloride channel, calcium activated, family member more 61.99(n)
    52.28(a)
      771009  XM_001234329.2  XP_001234330.2 
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia Str.151332 Transcribed sequence with weak similarity to protein more 75.9(n)    BX707609.1 
    zebrafish
    (Danio rerio)
    Actinopterygii si:ch211-116o3.36
    si:ch211-116o3.3
    46(a)
    many ↔ many
    15(14174040-14180344) ENSDARG00000086498


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CLCA2 gene
    CLCA42  CLCA12  
    3 SIMAP similar genes for CLCA2 using alignment to 1 protein entry:     CLCA2_HUMAN:
    CLCA3P    CLCA1    CLCA4

    CLCA2 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for CLCA2 (see all 834)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0431494
    A breast cancer sample4--see VAR_0431492 G E mis40--------
    rs1380326921,2
    C,Funtested186913377(+) TTTATC/TCCATT 2 P S mis12Minor allele frequency- T:0.00NA EU 5873
    rs1807738371,2
    --86887788(+) ACAGAA/GCCTTT 1 -- us2k10--------
    rs2001207151,2
    --86887800(+) AGCTG-/CCCACA 1 -- us2k10--------
    rs750630001,2
    C--86887802(+) CTGCC-/AACACC 1 -- us2k11Minor allele frequency- A:0.50CSA 2
    rs561849721,2
    C,F--86887851(+) AAAAAA/TCTAGG 1 -- us2k12Minor allele frequency- T:0.06WA 120
    rs1409478191,2
    --86887871(+) TCAGTC/TTGGGA 1 -- us2k10--------
    rs1446732581,2
    --86887954(+) CCCATA/TCTTCA 1 -- us2k10--------
    rs1385294061,2
    --86887967(+) GAGAGA/CACCAT 1 -- us2k10--------
    rs754354891,2
    C,F--86888070(+) TTTACA/CCTATA 1 -- us2k11Minor allele frequency- C:0.02NA 120

    HapMap Linkage Disequilibrium report for CLCA2 (86889769 - 86922241 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for CLCA2:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv871081CNV Loss21882294
    nsv521366CNV Loss19592680

    Human Gene Mutation Database (HGMD): CLCA2
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing CLCA2
    DNA2.0 Custom Variant and Variant Library Synthesis for CLCA2

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 604003    OMIM disorders: --

    17 diseases for CLCA2:    About MalaCards
    bestrophinopathy    breast and colorectal cancer    cystic fibrosis    sporadic breast cancer
    breast cancer    childhood leukemia    cholera    meningioma
    colorectal cancer    neuronitis    lung cancer    endotheliitis
    hiv-1    pancreatitis    hepatitis    leukemia
    prostatitis

    2 diseases from the University of Copenhagen DISEASES database for CLCA2:
    Cystic fibrosis     Bestrophinopathy

    CLCA2 for disorders           About GeneDecksing

    Genetic Association Database (GAD): CLCA2
    Human Genome Epidemiology (HuGE) Navigator: CLCA2 (5 documents)

    Export disorders for CLCA2 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for CLCA2 gene, integrated from 10 sources (see all 33):
    (articles sorted by number of sources associating them with CLCA2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification of three novel members of the calcium-dependent chloride channel (CaCC) family predominantly expressed in the digestive tract and trachea. (PubMed id 10437792)1, 2, 9 Agnel M.... Culouscou J.-M. (FEBS Lett. 1999)
    2. The quantification of hCLCA2 and colocalisation with integrin beta4 in stratified human epithelia. (PubMed id 15707651)1, 2, 9 Connon C.J.... Kinoshita S. (Acta Histochem. 2005)
    3. Risk of meningioma and common variation in genes related to innate immunity. (PubMed id 20406964)1, 4 Rajaraman P....Inskip P.D. (amp 2010)
    4. Polymorphisms in innate immunity genes and risk of childhood leukemia. (PubMed id 20438785)1, 4 Han S....Kang D. (Hum. Immunol. 2010)
    5. Evaluating new candidate SNPs as low penetrance risk factors in sporadic breast cancer: a two-stage Spanish case-control study. (PubMed id 18950845)1, 4 Vega A....Carracedo A. (Gynecol. Oncol. 2009)
    6. The putative chloride channel hCLCA2 has a single C-terminal transmembrane segment. (PubMed id 16873362)1, 2 Elble R.C.... Pauli B.U. (J. Biol. Chem. 2006)
    7. Gene expression and immunolocalisation of a calcium-activated chloride channel during the stratification of cultivated and developing corneal epithelium. (PubMed id 16158324)1, 2 Connon C.J.... Kinoshita S. (Cell Tissue Res. 2006)
    8. The breast cancer beta 4 integrin and endothelial human CLCA2 mediate lung metastasis. (PubMed id 11320086)1, 2 Abdel-Ghany M.... Pauli B.U. (J. Biol. Chem. 2001)
    9. Isolation and characterization of a Ca(2+)-activated chloride channel from human corneal epithelium. (PubMed id 11262615)1, 2 Itoh R.... Okubo K. (Curr. Eye Res. 2000)
    10. Molecular cloning and transmembrane structure of hCLCA2 from human lung, trachea, and mammary gland. (PubMed id 10362588)1, 2 Gruber A.D.... Pauli B.U. (Am. J. Physiol. 1999)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 9635 HGNC: 2016 AceView: CLCA2 Ensembl:ENSG00000137975 euGenes: HUgn9635
    ECgene: CLCA2 Kegg: 9635 H-InvDB: CLCA2

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for CLCA2 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for CLCA2 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

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    Patent Information for CLCA2 gene:
    Search GeneIP for patents involving CLCA2

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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