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CLCN3 Gene

protein-coding   GIFtS: 63
GCID: GC04P170541

Chloride Channel, Voltage-Sensitive 3

(Previous name: chloride channel 3)
  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, Voltage-Sensitive 31 2     ClC-32 3
Chloride Channel 31 2     CLC32
Chloride Channel Protein 32 3     H(+)/Cl(-) Exchange Transporter 32
Chloride Transporter ClC-32 3     

External Ids:    HGNC: 20211   Entrez Gene: 11822   Ensembl: ENSG000001095727   OMIM: 6005805   UniProtKB: P517903   

Export aliases for CLCN3 gene to outside databases

Previous GC identifers: GC04P171346 GC04P170970 GC04P171126 GC04P171237 GC04P170916 GC04P170778 GC04P166296


(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 CLCN3 Gene:
This gene encodes a member of the voltage-gated chloride channel (ClC) family. The encoded protein is present in
all cell types and localized in plasma membranes and in intracellular vesicles. It is a multi-pass membrane
protein which contains a ClC domain and two additional C-terminal CBS (cystathionine beta-synthase) domains. The
ClC domain catalyzes the selective flow of Cl- ions across cell membranes, and the CBS domain may have a
regulatory function. This protein plays a role in both acidification and transmitter loading of GABAergic
synaptic vesicles, and in smooth muscle cell activation and neointima formation. This protein is required for
lysophosphatidic acid (LPA)-activated Cl- current activity and fibroblast-to-myofibroblast differentiation. The
protein activity is regulated by Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) in glioma cells. Multiple
alternatively spliced transcript variants encoding different isoforms have been identified. (provided by RefSeq,
Aug 2011)

GeneCards Summary for CLCN3 Gene:
CLCN3 (chloride channel, voltage-sensitive 3) is a protein-coding gene. Diseases associated with CLCN3 include nephrolithiasis, and osteopetrosis. GO annotations related to this gene include PDZ domain binding and protein homodimerization activity. An important paralog of this gene is CLCN4.

UniProtKB/Swiss-Prot: CLCN3_HUMAN, P51790
Function: Mediates the exchange of chloride ions against protons. Functions as antiporter and contributes to the
acidification of the endosome and synaptic vesicle lumen, and may thereby affect vesicle trafficking and
exocytosis. May play an important role in neuronal cell function through regulation of membrane excitability by
protein kinase C. It could help neuronal cells to establish short-term memory

Gene Wiki entry for CLCN3 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_000004.12  NT_016354.20  NC_018915.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the CLCN3 gene promoter:
         AhR   Sox5   FOXC1   AML1a   FOXD3   POU3F2 (N-Oct-5b)   Cdc5   ATF6   C/EBPalpha   Gfi-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): CLCN3 promoter sequence
   Search Chromatin IP Primers for CLCN3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CLCN3


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

Entrez Gene cytogenetic band: 4q33   Ensembl cytogenetic band:  4q33   HGNC cytogenetic band: 4q

CLCN3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLCN3 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04P170541:  view genomic region     (about GC identifiers)

Start:
170,533,784 bp from pter      End:
170,644,824 bp from pter
Size:
111,041 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, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: CLCN3_HUMAN, P51790 (See protein sequence)
Recommended Name: H(+)/Cl(-) exchange transporter 3  
Size: 818 amino acids; 90966 Da
Subunit: Homo- or heterodimer. Isoform 2 interacts with GOPC, PDZK1 and SLC9A3R1/EBP50
Miscellaneous: The CLC channel family contains both chloride channels and proton-coupled anion transporters that
exchange chloride or another anion for protons. The presence of conserved gating glutamate residues is typical
for family members that function as antiporters (By similarity)
Sequence caution: Sequence=BAC54560.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=CAA55281.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: B7Z932 D3DP34 O14918 Q86Z21
Alternative splicing: 3 isoforms:  P51790-1   P51790-2   P51790-4   

Explore the universe of human proteins at neXtProt for CLCN3: NX_P51790

Explore proteomics data for CLCN3 at MOPED

Post-translational modifications: 

  • N-glycosylated1
  • Glycosylation2 at Asn177, Asn451, Asn479
  • Modification sites at PhosphoSitePlus

  • See CLCN3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (4 alternative transcripts): 
    NP_001230301.1  NP_001230303.1  NP_001820.2  NP_776297.2  

    ENSEMBL proteins: 
     ENSP00000425160   ENSP00000424603   ENSP00000261514   ENSP00000353857   ENSP00000425823  
     ENSP00000425323   ENSP00000422678   ENSP00000424540  
    Reactome Protein details: P51790

    CLCN3 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for CLCN3

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    Cloud-Clone Corp. ELISAs for CLCN3
    Cloud-Clone Corp. CLIAs for CLCN3


    (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-3
    ClC family

    4 InterPro protein domains:
     IPR014743 Cl-channel_core
     IPR000644 CBS_dom
     IPR002245 Cl_channel-3
     IPR001807 Cl-channel_volt-gated

    Graphical View of Domain Structure for InterPro Entry P51790

    ProtoNet protein and cluster: P51790

    3 Blocks protein domains:
    IPB000644 CBS domain
    IPB001807 Chloride channel signature
    IPB002245 CLC-3 chloride channel signature


    UniProtKB/Swiss-Prot: CLCN3_HUMAN, P51790
    Domain: Isoform 2 contains a C-terminal PDZ-binding motif mediating the interaction with GOPC
    Similarity: Belongs to the chloride channel (TC 2.A.49) family. ClC-3/CLCN3 subfamily
    Similarity: Contains 2 CBS domains


    CLCN3 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: CLCN3_HUMAN, P51790
    Function: Mediates the exchange of chloride ions against protons. Functions as antiporter and contributes to the
    acidification of the endosome and synaptic vesicle lumen, and may thereby affect vesicle trafficking and
    exocytosis. May play an important role in neuronal cell function through regulation of membrane excitability by
    protein kinase C. It could help neuronal cells to establish short-term memory

         Genatlas biochemistry entry for CLCN3:
    chloride voltage-gated channel 3,expressed in tissues derived from neuroectoderm

         Gene Ontology (GO): Selected molecular function terms (see all 11):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005216ion channel activity ----
    GO:0005244voltage-gated ion channel activity ----
    GO:0005247voltage-gated chloride channel activity IEA--
    GO:0005254chloride channel activity TAS12471024
    GO:0005515protein binding IPI12471024
         
    CLCN3 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for CLCN3:
     Cells with protrusions 

         14 MGI mutant phenotypes (inferred from 3 alleles(MGI details for Clcn3):
     adipose tissue  behavior/neurological  digestive/alimentary  growth/size/body  hematopoietic system 
     homeostasis/metabolism  immune system  liver/biliary system  mortality/aging  nervous system 
     renal/urinary system  reproductive system  skeleton  vision/eye 

    CLCN3 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for CLCN3: Clcn3tm1Tjj Clcn3tm1Lamb Clcn3tm1Suc

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for CLCN3
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for CLCN3

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for CLCN3
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for CLCN3

    miRNA
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    miRTarBase miRNAs that target CLCN3:
    hsa-mir-548b-3p (MIRT040507), hsa-mir-335-5p (MIRT018874), hsa-mir-1 (MIRT002737), hsa-mir-148b-3p (MIRT019489)

    Block miRNA regulation of human, mouse, rat CLCN3 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate CLCN3 (see all 18):
    hsa-miR-3673 hsa-miR-16-2* hsa-miR-539 hsa-miR-578 hsa-miR-583 hsa-miR-23a hsa-miR-24 hsa-miR-613
    SwitchGear 3'UTR luciferase reporter plasmidCLCN3 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for CLCN3
    Predesigned siRNA for gene silencing in human, mouse, rat CLCN3

    Gene Editing
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    Clone
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    GenScript: all cDNA clones in your preferred vector (see all 2): CLCN3 (NM_001829)
    Browse Sino Biological Human cDNA Clones
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat CLCN3

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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CLCN3


    (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
    CLCN3_HUMAN, P51790: Isoform 1: Membrane; Multi-pass membrane protein. Early endosome membrane; Multi-pass
    membrane protein. Late endosome membrane; Multi-pass membrane protein. Cytoplasmic vesicle, secretory vesicle
    membrane; Multi-pass membrane protein (By similarity). Note=Isoform 1 is localized mainly in early and late
    endosomes
    CLCN3_HUMAN, P51790: Isoform 2: Membrane; Multi-pass membrane protein. Early endosome membrane; Multi-pass
    membrane protein. Late endosome membrane; Multi-pass membrane protein. Golgi apparatus membrane; Multi-pass
    membrane protein. Note=Isoform 2 partially colocalized with isoform 1 but is mainly enriched in the Golgi
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    endosome5
    golgi apparatus5
    plasma membrane3
    cytosol1
    extracellular1
    peroxisome1

    Gene Ontology (GO): Selected cellular component terms (see all 14):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000139Golgi membrane IEA--
    GO:0005622intracellular ----
    GO:0005769early endosome IDA12471024
    GO:0005770late endosome IDA12471024
    GO:0005794Golgi apparatus IDA12471024

    CLCN3 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 CLCN3 About    
    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

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    5 Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for CLCN3
        Cholera Infection
    Hepatic ABC Transporters
    PKA Signaling
    cAMP Pathway
    Activation of cAMP-Dependent PKA

    1 Reactome Pathway for CLCN3
        Stimuli-sensing channels



    CLCN3 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Array including CLCN3: 
              Neuronal Ion Channels in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for CLCN3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 10)

    Selected Interacting proteins for CLCN3 (P517902, 3 ENSP000002615144) via UniProtKB, MINT, STRING, and/or I2D (see all 12)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    GOPCQ9HD262, 3, ENSP000003574844MINT-1783634 MINT-1790205 I2D: score=3 STRING: ENSP00000357484
    SLC9A3R1O147452, 3, ENSP000002626134MINT-1783705 MINT-1783541 I2D: score=3 STRING: ENSP00000262613
    CFTRP135692, 3, ENSP000000030844MINT-1783848 I2D: score=1 STRING: ENSP00000003084
    PDZK1Q5T2W12, 3, ENSP000003421434MINT-1783611 MINT-1783832 MINT-1790188 I2D: score=3 STRING: ENSP00000342143
    CLCN3P517902MINT-1783371 MINT-1783519 MINT-1783481
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 10):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006810transport TAS7665160
    GO:0006811ion transport ----
    GO:0006821chloride transport ----
    GO:0006885regulation of pH TAS12471024
    GO:0034220ion transmembrane transport TAS--

    CLCN3 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 

    Browse Tocris compounds for CLCN3

    1 HMDB Compound for CLCN3    About this table
    CompoundSynonyms CAS #PubMed Ids
    ChlorineCl2 (see all 13)16887-00-6--

    1 IUPHAR Ligand for CLCN3 (ClC-3)    About this table
    LigandTypeActionAffinityPubmed IDs
    phloretin
    Channel blockerNone4.5--

    6 Novoseek inferred chemical compound relationships for CLCN3 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    chloride 78.3 42 12916350 (4), 11278960 (3), 15127135 (3), 18359479 (3) (see all 17)
    dids 68 3 17360969 (1)
    thapsigargin 41.1 5 16520896 (2)
    nadph 33.8 1 17673675 (1)
    calcium 0 3 11278960 (1), 20139089 (1)
    superoxide 0 4 17360969 (2)



    CLCN3 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,
    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 CLCN3 gene (4 alternative transcripts): 
    NM_001243372.1  NM_001243374.1  NM_001829.3  NM_173872.3  

    Unigene Cluster for CLCN3:

    Chloride channel, voltage-sensitive 3
    Hs.481186  [show with all ESTs]
    Unigene Representative Sequence: NM_173872
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000511092 ENST00000513761(uc003ish.3 uc003isi.3 uc011cka.2 uc011cjz.2 uc003isj.2)
    ENST00000347613 ENST00000360642 ENST00000512813 ENST00000506924 ENST00000507875
    ENST00000502998 ENST00000515420 ENST00000504131
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    Selected qRT-PCR Assays for microRNAs that regulate CLCN3 (see all 18):
    hsa-miR-3673 hsa-miR-16-2* hsa-miR-539 hsa-miR-578 hsa-miR-583 hsa-miR-23a hsa-miR-24 hsa-miR-613
    SwitchGear 3'UTR luciferase reporter plasmidCLCN3 3' UTR sequence
    Inhib. RNA
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    GenScript: all cDNA clones in your preferred vector (see all 2): CLCN3 (NM_001829)
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      QuantiFast Probe-based Assays in human, mouse, rat CLCN3

    Additional mRNA sequence: 

    AB019542.1 AF029346.1 AF086418.1 AF172729.1 AK127483.1 AK304362.1 AL117599.1 BC026256.1 
    BC054877.1 BC058818.1 BC136510.1 BX647119.1 X78520.1 

    19 DOTS entries:

    DT.451815  DT.100040100  DT.101973138  DT.101961549  DT.100788498  DT.100788495  DT.97803884  DT.91695921 
    DT.102828744  DT.99956924  DT.100788493  DT.97856779  DT.100662492  DT.121268695  DT.91843148  DT.92424602 
    DT.95235314  DT.99987740  DT.92462664 

    Selected AceView cDNA sequences (see all 368):

    BE048469 AA250861 H99764 T35218 BM791752 BF589537 AI400370 AI073875 
    CA941048 BE042776 AI923105 AI564120 BM972665 CN484138 AA417185 F08200 
    AF172729 CR593231 BQ433763 BQ186265 AI201396 BX509936 AI754713 BM993572 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for CLCN3 (see all 7)    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18a · 18b
    SP1:              -                 -     -                                   -                                                                           
    SP2:              -                 -     -                                   -                                                           -               
    SP3:                                                                          -                                                                           
    SP4:                                                                                                                                                      
    SP5:                                                                                                                                                      


    ECgene alternative splicing isoforms for CLCN3

    (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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    CLCN3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CACCACAACA
    CLCN3 Expression
    About this image


    CLCN3 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Brain (Nervous System)
             Cerebral Cortex
     
     Colon (Gastrointestinal Tract)
    CLCN3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CLCN3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.481186

    UniProtKB/Swiss-Prot: CLCN3_HUMAN, P51790
    Tissue specificity: Expressed primarily in tissues derived from neuroectoderm. Within the brain, its expression is
    particularly evident in the hippocampus, olfactory cortex, and olfactory bulb. Highly expressed in aortic and
    coronary vascular smooth muscle cells, and aortic endothelial cells. Also expressed in tracheal and alveolar
    epithelial cells, and intima and media of the pulmonary vessels. Expressed in bronchus and colon (at protein
    level)

        Pathway & Disease-focused RT2 Profiler PCR Array including CLCN3: 
              Neuronal Ion Channels in human mouse rat

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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 and fungi.

    Orthologs for CLCN3 gene from Selected species (see all 21)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Clcn31 , 5 chloride channel 31, 5 92.3(n)1
    98.61(a)1
      8 (30.90 cM)5
    127251  NM_173874.11  NP_776299.11 
     609103895 
    chicken
    (Gallus gallus)
    Aves CLCN31 chloride channel, voltage-sensitive 3 87.3(n)
    98.04(a)
      422432  XM_420400.4  XP_420400.2 
    lizard
    (Anolis carolinensis)
    Reptilia CLCN36
    chloride channel, voltage-sensitive 3
    95(a)
    1 ↔ 1
    GL343216.1(747774-800470)
    African clawed frog
    (Xenopus laevis)
    Amphibia Clcn32 putative chloride channel ClC-3 75.51(n)    Y09941.2 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.103032 Transcribed sequence with moderate similarity to protein more 73.4(n)    57043120 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG52843
    ClC-c1
    chloride channel3
    Chloride channel-c1
    59(a)3
    60.65(n)1
    63.47(a)1
      72D53
    397591  NM_140577.21  NP_648834.11 
    worm
    (Caenorhabditis elegans)
    Secernentea clh-51 clh-5 57.24(n)
    55.51(a)
      174449  NM_063539.5  NP_495940.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes GEF1(YJR040W)4
    GEF11
    Voltage-gated chloride channel localized to the golgi, more4
    GEF11
    47.35(n)1
    35.51(a)1
      10(507746-510085)4
    8534971, 4  NP_012574.11, 4 


    ENSEMBL Gene Tree for CLCN3 (if available)
    TreeFam Gene Tree for CLCN3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CLCN3 gene
    CLCN42  CLCN62  CLCNKB2  CLCN52  CLCN12  CLCN72  CLCNKA2  CLCN22  
    4 SIMAP similar genes for CLCN3 using alignment to 7 protein entries:     CLCN3_HUMAN (see all proteins):
    CLCN5    CLCN4    CLCN1    KIAA1651

    CLCN3 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for CLCN3
    PGOHUM00000235971


    (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 CLCN3 (see all 1992)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 4 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1389975281,2
    C--166305104(+) ATATT-/CTGT  
     ATCTTGA
    CTGTA
    3 -- int10--------
    rs581927241,2
    C--166305111(+) GTATC-/TTGA  
     CTGTATC
    AATGT
    3 -- int10--------
    rs58640001,2
    C--166308128(+) GTATG-/ATCCA 
            
    GGCAG
    3 -- int10--------
    rs1383928171,2
    C--166313515(+) ACAAA-/CACCACCA 3 -- cds10--------
    rs1458262411,2
    C--166313516(+) CAAAC-/CACACCAC 3 -- cds10--------
    rs340460471,2
    C--166324970(+) AAAAAA/-AAAAA 3 -- int11Minor allele frequency- -:0.00NA 2
    rs670079321,2
    C--166339064(+) ATATA-/TGTGTGT 4 -- int10--------
    rs1136616911,2
    C--166348154(+) AAATAAAT/-GATAG 4 -- int11Minor allele frequency- -:0.50CSA 2
    rs119327591,2
    C,H--166378754(+) aaaaaG/Aaagaa 4 -- int1 trp31Minor allele frequency- A:0.00NA 2
    rs759659731,2
    F--166386371(+) GCACAC/TCATCC 4 -- int12Minor allele frequency- T:0.50NA 8

    HapMap Linkage Disequilibrium report for CLCN3 (170533784 - 170644824 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for CLCN3:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv4600CNV Insertion18451855
    nsv518832CNV Loss19592680

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing CLCN3
    DNA2.0 Custom Variant and Variant Library Synthesis for CLCN3

    (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: 600580    OMIM disorders: --

    19 diseases for CLCN3:    
    About MalaCards
    nephrolithiasis    osteopetrosis    epididymitis    cystic fibrosis
    nasopharyngitis    allergic rhinitis    rhinitis    malignant glioma
    cholera    asthma    pneumonia    prostate cancer
    prostatitis    retinitis    hepatocellular carcinoma    endotheliitis
    neuronitis    hepatitis    malaria


    CLCN3 for disorders           About GeneDecksing

    5 Novoseek inferred disease relationships for CLCN3 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    cystic fibrosis 42.7 3 10932070 (1), 10087150 (1)
    glioma 23.6 5 20139089 (3), 12843258 (2)
    carcinoma 0 1 15947107 (1)
    prostate cancer 0 1 15256454 (1)
    cancer 0 2 15127135 (1), 18359479 (1)

    Genetic Association Database (GAD): CLCN3

    Export disorders for CLCN3 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 CLCN3 gene, integrated from 10 sources (see all 81):
    (articles sorted by number of sources associating them with CLCN3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The PDZ-binding chloride channel ClC-3B localizes to the Golgi and associates with cystic fibrosis transmembrane conductance regulator- interacting PDZ proteins. (PubMed id 12471024)1, 2, 9 Gentzsch M.... Riordan J.R. (J. Biol. Chem. 2003)
    2. ClC-3B, a novel ClC-3 splicing variant that interacts with EBP50 and facilitates expression of CFTR-regulated ORCC. (PubMed id 11967229)1, 2 Ogura T.... Inagaki N. (FASEB J. 2002)
    3. Regulation of human CLC-3 channels by multifunctional Ca2+/calmodulin-dependent protein kinase. (PubMed id 11274166)1, 2 Huang P....Nelson D.J. (J. Biol. Chem. 2001)
    4. Expression of CLCN voltage-gated chloride channel genes in human blood vessels. (PubMed id 10198195)1, 2 Lamb F.S....Schutte B.C. (J. Mol. Cell. Cardiol. 1999)
    5. Ion transporters and receptors in cDNA libraries from lens and cornea epithelia. (PubMed id 9678416)1, 2 Shepard A.R. and Rae J.L. (Curr. Eye Res. 1998)
    6. Characterization of a human and murine gene (CLCN3) sharing similarities to voltage-gated chloride channels and to a yeast integral membrane protein. (PubMed id 7665160)1, 2 Borsani G.... Ballabio A. (Genomics 1995)
    7. ClC-3 is required for LPA-activated Cl- current activity and fibroblast-to-myofibroblast differentiation. (PubMed id 18077605)1, 9 Yin Z....Watsky M.A. (Am. J. Physiol., Cell Physiol. 2008)
    8. Molecular interaction and functional regulation of ClC-3 by Ca2+/calmodulin-dependent protein kinase II (CaMKII) in human malignant glioma. (PubMed id 20139089)1, 9 Cuddapah V.A. and Sontheimer H. (J. Biol. Chem. 2010)
    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. Overexpression of CLC-3 in HEK293T cells yields novel currents that are pH dependent. (PubMed id 17977943)1, 9 Matsuda J.J....Lamb F.S. (Am. J. Physiol., Cell Physiol. 2008)

    (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: 1182 HGNC: 2021 AceView: CLCN3 Ensembl:ENSG00000109572 euGenes: HUgn1182
    ECgene: CLCN3 H-InvDB: CLCN3

    (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 CLCN3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for CLCN3 gene:
    Search GeneIP for patents involving CLCN3

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



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