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CLCN2 Gene

protein-coding   GIFtS: 67
GCID: GC03M184063

Chloride Channel, Voltage-Sensitive 2

(Previous name: chloride channel 2)
  See CLCN2-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, Voltage-Sensitive 21 2     CLC22
Chloride Channel 21 2     ECA32
ECA22 5     EGI32
EGI112 5     EJM62
EGMA2 5     Chloride Channel Protein 22
EJM82 5     clC-22
LKPAT2 5     ClC-23
CIC-22     

External Ids:    HGNC: 20201   Entrez Gene: 11812   Ensembl: ENSG000001148597   OMIM: 6005705   UniProtKB: P517883   

Export aliases for CLCN2 gene to outside databases

Previous GC identifers: GC03P180523 GC03M185057 GC03M185466 GC03M185385 GC03M185546 GC03M181470


(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 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 leukoencephalopathy with ataxia, and clcn2-related juvenile myoclonic epilepsy. GO annotations related to this gene include adenyl nucleotide binding and voltage-gated chloride channel activity. An important paralog of this gene is CLCN4.

UniProtKB/Swiss-Prot: CLCN2_HUMAN, P51788
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 Wiki entry for CLCN2 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_000003.12  NT_005612.17  NC_018914.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the CLCN2 gene promoter:
         CREB   AP-1   STAT3   STAT5A   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCLCN2 promoter sequence
   Search Chromatin IP Primers for CLCN2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CLCN2


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

Entrez Gene cytogenetic band: 3q27.1   Ensembl cytogenetic band:  3q27.1   HGNC cytogenetic band: 3q27.1

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

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03M184063:  view genomic region     (about GC identifiers)

Start:
184,063,973 bp from pter      End:
184,079,439 bp from pter
Size:
15,467 bases      Orientation:
minus 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: CLCN2_HUMAN, P51788 (See protein sequence)
Recommended Name: Chloride channel protein 2  
Size: 898 amino acids; 98535 Da
Miscellaneous: 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 caution: Sequence=AAH21578.1; Type=Erroneous translation; Note=Wrong choice of frame;
Secondary accessions: B4DQT9 B4DZ58 E9PBD9 E9PCD2 O14864 Q6IPA9 Q8WU13
Alternative splicing: 5 isoforms:  P51788-1   P51788-2   P51788-3   P51788-4   P51788-5   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for CLCN2: NX_P51788

Explore proteomics data for CLCN2 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See CLCN2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (4 alternative transcripts): 
    NP_001164558.1  NP_001164559.1  NP_001164560.1  NP_004357.3  

    ENSEMBL proteins: 
     ENSP00000265593   ENSP00000345056   ENSP00000396231   ENSP00000400425   ENSP00000391928  
     ENSP00000412226  
    Reactome Protein details: P51788

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    CLCN: Ion channels / Chloride channels : Voltage-sensitive

    IUPHAR Guide to PHARMACOLOGY protein family classification: ClC-2
    ClC family

    4 InterPro protein domains:
     IPR014743 Cl-channel_core
     IPR000644 CBS_dom
     IPR002244 Cl-channel-2
     IPR001807 Cl-channel_volt-gated

    Graphical View of Domain Structure for InterPro Entry P51788

    ProtoNet protein and cluster: P51788

    3 Blocks protein domains:
    IPB000644 CBS domain
    IPB001807 Chloride channel signature
    IPB002244 CLC-2 chloride channel signature


    UniProtKB/Swiss-Prot: CLCN2_HUMAN, P51788
    Similarity: Belongs to the chloride channel (TC 2.A.49) family. ClC-2/CLCN2 subfamily
    Similarity: Contains 2 CBS domains


    Find genes that share domains with CLCN2           About GenesLikeMe


    (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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: CLCN2_HUMAN, P51788
    Function: Voltage-gated chloride channel. Chloride channels have several functions including the regulation of
    cell volume; membrane potential stabilization, signal transduction and transepithelial transport

         Genatlas biochemistry entry for CLCN2:
    chloride voltage-gated channel 2,widely expressed

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005216ion channel activity ----
    GO:0005247voltage-gated chloride channel activity IEA--
    GO:0030554adenyl nucleotide binding IEA--
         
    Find genes that share ontologies with CLCN2           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for CLCN2:
     Increased S DNA content 

         11 MGI mutant phenotypes (inferred from 3 alleles(MGI details for Clcn2):
     behavior/neurological  cardiovascular system  digestive/alimentary  endocrine/exocrine gland  hematopoietic system 
     homeostasis/metabolism  immune system  nervous system  pigmentation  reproductive system 
     vision/eye 

    Find genes that share phenotypes with CLCN2           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for CLCN2: Clcn2tm1Tjj Clcn2tm1Mlv

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    hsa-miR-3163 hsa-miR-3653 hsa-miR-216b hsa-miR-138-2* hsa-miR-1273d hsa-miR-3658 hsa-miR-3675-3p hsa-miR-889
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    (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
    CLCN2_HUMAN, P51788: Membrane; Multi-pass membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane4
    peroxisome1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane TAS--
    GO:0016020membrane ----
    GO:0034707chloride channel complex IEA--

    Find genes that share ontologies with CLCN2           About GenesLikeMe


    (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 CLCN2 About   (see all 6)  
    See pathways by source

    SuperPathContained pathways About
    1Activation of cAMP-Dependent PKA
    Activation of cAMP-Dependent PKA0.77
    PKA Signaling0.56
    cAMP Pathway0.77
    2Ion channel transport
    Ion channel transport0.58
    Stimuli-sensing channels0.58
    3Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds
    Transmembrane transport of small molecules0.47
    4Hepatic ABC Transporters
    Hepatic ABC Transporters0.41
    5Neuropathic Pain-Signaling in Dorsal Horn Neurons
    Cholera Infection0.40


    Find genes that share SuperPaths with CLCN2           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    5 Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for CLCN2
        Cholera Infection
    Hepatic ABC Transporters
    PKA Signaling
    cAMP Pathway
    Activation of cAMP-Dependent PKA

    1 Reactome Pathway for CLCN2
        Stimuli-sensing channels


    1 Kegg Pathway  (Kegg details for CLCN2):
        Mineral absorption

        Pathway & Disease-focused RT2 Profiler PCR Array including CLCN2: 
              Neuronal Ion Channels in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for CLCN2

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

    4 Interacting proteins for CLCN2 (ENSP000002655934) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CRBNENSP000002319484STRING: ENSP00000231948
    ASNA1ENSP000003498874STRING: ENSP00000349887
    PPP1CAENSP000003260314STRING: ENSP00000326031
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006810transport TAS7795595
    GO:0006821chloride transport ----
    GO:0034220ion transmembrane transport TAS--
    GO:0044070regulation of anion transport TAS7795595
    GO:0055085transmembrane transport TAS--

    Find genes that share ontologies with CLCN2           About GenesLikeMe



    (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 

    Browse Tocris compounds for CLCN2

    1 HMDB Compound for CLCN2    About this table
    CompoundSynonyms CAS #PubMed Ids
    ChlorineCl2 (see all 13)16887-00-6--

    1 DrugBank Compound for CLCN2    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    Lubiprostone-- 136790-76-6targetinducer15991886 17509103 17053162 17263187 18686757 17413599 11752352 20345211 19236188 17519292

    8 IUPHAR Ligands for CLCN2 (ClC-2)    About this table
    LigandTypeActionAffinityPubmed IDs
    GaTx2
    Channel blockerNone10.8--
    omeprazole
    ActivatorNone10.8--
    Cd2+
    Channel blockerNone10.8--
    lubiprostone
    ActivatorNone10.8--
    DPC
    Channel blockerNone10.8--
    arachidonic acid
    ActivatorNone10.8--
    Zn2+
    Channel blockerNone10.8--
    NPPB
    Channel blockerNone10.8--

    6 Novoseek inferred chemical compound relationships for CLCN2 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    lubiprostone 95.8 13 19444393 (1), 15991886 (1), 17263187 (1), 19577749 (1) (see all 10)
    chloride 84.5 74 11068136 (5), 11883714 (3), 11076524 (2), 11104687 (2) (see all 31)
    halide 52.3 1 10050002 (1)
    atp 0 4 17620322 (4)
    sodium 0 1 19090733 (1)
    hydrogen 0 1 16034421 (1)



    Find genes that share compounds with CLCN2           About GenesLikeMe



    (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,
    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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for CLCN2 gene (4 alternative transcripts): 
    NM_001171087.2  NM_001171088.2  NM_001171089.2  NM_004366.5  

    Unigene Cluster for CLCN2:

    Chloride channel, voltage-sensitive 2
    Hs.436847  [show with all ESTs]
    Unigene Representative Sequence: NM_004366
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000265593(uc003foh.3 uc010hya.2 uc003foi.3 uc011brl.2 uc011brm.2)
    ENST00000344937 ENST00000430397 ENST00000434054 ENST00000457512 ENST00000491162
    ENST00000485667(uc011brn.1) ENST00000475279 ENST00000465231 ENST00000423355

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    Additional mRNA sequence: 

    AF026004.1 AK298952.1 AK302759.1 BC021578.1 BC072004.1 

    7 DOTS entries:

    DT.100711929  DT.102823139  DT.91722254  DT.120865053  DT.86853834  DT.91722229  DT.316476 

    Selected AceView cDNA sequences (see all 83):

    BC021578 AI681838 AI540201 AF026004 BM970808 CD618592 BX089717 BQ927284 
    F04058 BU616497 F07799 BM971760 BQ952887 BM716763 BM674392 NM_004366 
    AI570993 BQ924835 BC072004 CD618582 AA412696 AW207669 AI291208 CD618581 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for CLCN2    About this scheme

    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:                                                                          -     -                                                                           
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            

    ExUns: 23 ^ 24
    SP1:            
    SP2:            
    SP3:            
    SP4:            


    ECgene alternative splicing isoforms for CLCN2

    (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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    CLCN2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CCCGTCAGCC
    CLCN2 Expression
    About this image


    CLCN2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 4) fully expand
     
     Brain (Nervous System)    fully expand to see all 2 entries
             Cerebral Cortex
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
     
     Liver (Hepatobiliary System)
             Perivenous Hepatocytes Liver Lobule
    CLCN2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CLCN2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.436847

    UniProtKB/Swiss-Prot: CLCN2_HUMAN, P51788
    Tissue specificity: Ubiquitously expressed. Moderately expressed in aortic and coronary vascular smooth muscle
    cells and expressed at a low level in aortic endothelial cells

        Pathway & Disease-focused RT2 Profiler PCR Array including CLCN2: 
              Neuronal Ion Channels in human mouse rat

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    In Situ
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    (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 animals.

    Orthologs for CLCN2 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Clcn21 , 5 chloride channel 21, 5 88.09(n)1
    94.49(a)1
      16 (12.50 cM)5
    127241  NM_009900.21  NP_034030.21 
     207029645 
    chicken
    (Gallus gallus)
    Aves CLCN21 chloride channel, voltage-sensitive 2 75.12(n)
    77.37(a)
      425295  XM_423073.4  XP_423073.4 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    --
    84(a)
    76(a)
    1 ↔ many
    1 ↔ many
    GL343504.1(467817-554890)
    GL343245.1(8669-40682)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia clcn21 chloride channel, voltage-sensitive 2 69.43(n)
    77.22(a)
      100488889  XM_004914409.1  XP_004914466.1 
    zebrafish
    (Danio rerio)
    Actinopterygii BM264655.12   -- 72.24(n)    BM264655.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta ClC-a1 Chloride channel-a 55.94(n)
    52.8(a)
      41428  NM_001104282.3  NP_001097752.1 
    worm
    (Caenorhabditis elegans)
    Secernentea clh-31 , 3 Chloride channel protein3
    clh-31
    42(a)3
    49.54(n)1
    46.8(a)1
      II(7218345-7222930)3
    1741871  NM_001026889.21  NP_001022060.11 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CLCN2 gene
    CLCN42  CLCN62  CLCNKB2  CLCN52  CLCN12  CLCN72  CLCN32  CLCNKA2  
    3 SIMAP similar genes for CLCN2 using alignment to 2 protein entries:     CLCN2_HUMAN (see all proteins):
    CLCN1    CLCNKA    CLCNKB

    Find genes that share paralogs with CLCN2           About GenesLikeMe



    (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 CLCN2 (see all 535)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1378526821,2
    C,Fother1183937813(-) GTACCG/AGGTGC 8 /Q /R mis12Minor allele frequency- A:0.00NA EU 4563
    rs713183691,2,,4
    C,Fother1183941714(+) TGTTCC/TGGGAT 8 Q R mis14Minor allele frequency- T:0.00NA EU 5831
    rs1158140701,2
    C,F--183929729(+) CTCCTA/TGGATG 4 -- ds50011Minor allele frequency- T:0.03WA 118
    rs1382769691,2
    --183929732(+) CTAGGA/TTGTGC 4 -- ds50010--------
    rs1419135271,2
    --183929783(+) TTCACA/GCAGAG 4 -- ds50010--------
    rs1118753521,2
    C--183929884(+) CAGGGG/ATGGCC 4 -- ds50012Minor allele frequency- A:0.03NA 122
    rs177743961,2
    C,F,H--183930015(+) AAGGCT/CACAGT 4 -- ds500115Minor allele frequency- C:0.06NA EA NS 1582
    rs99441,2
    C,F,A,H--183930031(-) TGGGGC/TGGGGC 4 -- ds500125Minor allele frequency- T:0.26MN EA NS NA WA CSA 3077
    rs1502442351,2
    C--183930339(+) TAAACC/TCATCT 4 -- ut310--------
    rs1846696601,2
    --183930345(+) CATCTC/TAGTTC 4 -- ut310--------

    HapMap Linkage Disequilibrium report for CLCN2 (184063973 - 184079439 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for CLCN2:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2422400CNV Duplication17116639
    nsv878060CNV Loss21882294
    nsv829813CNV Loss17160897
    nsv878057CNV Loss21882294

    Human Gene Mutation Database (HGMD): CLCN2
    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing CLCN2
    DNA2.0 Custom Variant and Variant Library Synthesis for CLCN2

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 600570   
    OMIM disorders: 607628  615651  
    UniProtKB/Swiss-Prot: CLCN2_HUMAN, P51788
  • 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

  • 11 diseases for CLCN2:    
    About MalaCards
    leukoencephalopathy with ataxia    clcn2-related juvenile myoclonic epilepsy    epilepsy, juvenile absence, susceptibility to, 2    constipation
    epilepsy, idiopathic generalized 11    epilepsy, juvenile myoclonic 8    irritable bowel syndrome    megalencephalic leukoencephalopathy with subcortical cysts
    juvenile absence epilepsy    idiopathic generalized epilepsy    cystic fibrosis

    2 diseases from the University of Copenhagen DISEASES database for CLCN2:
    Juvenile absence epilepsy     Idiopathic generalized epilepsy

    Find genes that share disorders with CLCN2           About GenesLikeMe

    5 Novoseek inferred disease relationships for CLCN2 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    cystic fibrosis 57.8 7 11401826 (2), 19926984 (1), 15507145 (1), 10932070 (1) (see all 5)
    malignant glioma 25.1 2 16831268 (1), 12843258 (1)
    epilepsy 20.2 7 19191339 (2), 16526942 (1), 17008177 (1)
    shock 5.99 3 11104687 (1), 15939036 (1), 9929373 (1)
    glioma 1.95 6 12843258 (3), 16831268 (2)

    Genetic Association Database (GAD): CLCN2
    Human Genome Epidemiology (HuGE) Navigator: CLCN2 (5 documents)

    Export disorders for CLCN2 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 CLCN2 gene, integrated from 10 sources (see all 108):
    (articles sorted by number of sources associating them with CLCN2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Two novel CLCN2 mutations accelerating chloride channel deactivation are associated with idiopathic generalized epilepsy. (PubMed id 19191339)1, 2, 4, 9 Saint-Martin C....Depienne C. (Hum. Mutat. 2009)
    2. Cloning of a putative human voltage-gated chloride channel (ClC-2) cDNA widely expressed in human tissues. (PubMed id 7795595)1, 2, 3 Cid L.P....Cutting G.R. (Hum. Mol. Genet. 1995)
    3. CLC-2 single nucleotide polymorphisms (SNPs) as potential modifiers of cystic fibrosis disease severity. (PubMed id 15507145)1, 4, 9 Blaisdell C.J....Stine O.C. (BMC Med. Genet. 2004)
    4. Alterations in the cytoplasmic domain of CLCN2 result in altered gating kinetics. (PubMed id 17762171)1, 2, 9 Paul J.... Kun J.F.J. (Cell. Physiol. Biochem. 2007)
    5. Expression of CLCN voltage-gated chloride channel genes in human blood vessels. (PubMed id 10198195)1, 2, 9 Lamb F.S....Schutte B.C. (J. Mol. Cell. Cardiol. 1999)
    6. Mutations in the CLCN2 gene are a rare cause of idiopathic generalized epilepsy syndromes. (PubMed id 16932951)1, 4 Stogmann E....Zimprich A. (Neurogenetics 2006)
    7. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    8. Association between Hsp90 and the ClC-2 chloride channel upregulates channel function. (PubMed id 16049054)1, 9 Hinzpeter A....Fritsch J. (Am. J. Physiol., Cell Physiol. 2006)
    9. Possible role of transforming growth factor beta and interleukin-4 in the up-regulation of CLC-2 and CLC-3 in chronic rhinosinusitis. (PubMed id 17882904)1, 9 Li H....Xu G. (Am J Rhinol 2007)
    10. Distribution of ClC-2 chloride channel in rat and human epithelial tissues. (PubMed id 11880269)1, 9 Lipecka J....Fritsch J. (Am. J. Physiol., Cell Physiol. 2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    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: 1181 HGNC: 2020 AceView: CLCN2 Ensembl:ENSG00000114859 euGenes: HUgn1181
    ECgene: CLCN2 Kegg: 1181 H-InvDB: CLCN2

    (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)
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    NameDescription
    PharmGKB entry for CLCN2 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=CLCN2[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for CLCN2 gene:
    Search GeneIP for patents involving CLCN2

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



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