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CLCN5 Gene

protein-coding   GIFtS: 65
GCID: GC0XP049687

Chloride Channel, Voltage-Sensitive 5

(Previous names: nephrolithiasis 2, X-linked, nephrolithiasis 1 (X-linked),...)
(Previous symbols: NPHL2, NPHL1)
  See CLCN5-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 51 2     Nephrolithiasis 1 (X-Linked)1
NPHL11 2 5     Nephrolithiasis 2, X-Linked1
NPHL21 2 5     CLC52
CLCK22 3 5     XLRH2
Chloride Transporter ClC-52 3     XRN2
ClC-52 3     H(+)/Cl(-) Exchange Transporter 52
DENTS2 5     hCIC-K22
Chloride Channel 51     Voltage-Gated Chloride Ion Channel CLCN52
Dent Disease1     Chloride Channel Protein 53

External Ids:    HGNC: 20231   Entrez Gene: 11842   Ensembl: ENSG000001713657   OMIM: 3000085   UniProtKB: P517953   

Export aliases for CLCN5 gene to outside databases

Previous GC identifers: GC0XP048431 GC0XP047889 GC0XP048604 GC0XP048751 GC0XP049390 GC0XP049573 GC0XP047156


(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 CLCN5 Gene:
This gene encodes a member of the ClC family of chloride ion channels and ion transporters. The encoded protein is
primarily localized to endosomal membranes and may function to facilitate albumin uptake by the renal proximal
tubule. Mutations in this gene have been found in Dent disease and renal tubular disorders complicated by
nephrolithiasis. Alternatively spliced transcript variants have been found for this gene. (provided by RefSeq,
Jan 2013)

GeneCards Summary for CLCN5 Gene:
CLCN5 (chloride channel, voltage-sensitive 5) is a protein-coding gene. Diseases associated with CLCN5 include dent's disease, and nephrolithiasis. GO annotations related to this gene include antiporter activity and chloride channel activity. An important paralog of this gene is CLCN7.

UniProtKB/Swiss-Prot: CLCN5_HUMAN, P51795
Function: Proton-coupled chloride transporter. Functions as antiport system and exchanges chloride ions against
protons. Important for normal acidification of the endosome lumen. May play an important role in renal tubular
function

Gene Wiki entry for CLCN5 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 at NCBI GenBank:
NC_000023.10  NC_018934.2  NT_079573.5  
Regulatory elements:
   Regulatory transcription factor binding sites in the CLCN5 gene promoter:
         AP-1   ATF-2   E2F-2   CREB   E2F   E2F-1   deltaCREB   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCLCN5 promoter sequence
   Search Chromatin IP Primers for CLCN5

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CLCN5


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

Entrez Gene cytogenetic band: Xp11.23-p11.22   Ensembl cytogenetic band:  Xp11.23   HGNC cytogenetic band: Xp11.23-p11.22

CLCN5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CLCN5 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XP049687:  view genomic region     (about GC identifiers)

Start:
49,687,225 bp from pter      End:
49,863,892 bp from pter
Size:
176,668 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: CLCN5_HUMAN, P51795 (See protein sequence)
Recommended Name: H(+)/Cl(-) exchange transporter 5  
Size: 746 amino acids; 83147 Da
Subunit: Interacts with NEDD4 and NEDD4L
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
2 PDB 3D structures from and Proteopedia for CLCN5:
2J9L (3D)        2JA3 (3D)    
Secondary accessions: A1L475 B3KPN6 Q5JQD5 Q7RTN8
Alternative splicing: 2 isoforms:  P51795-1   P51795-2   

Explore the universe of human proteins at neXtProt for CLCN5: NX_P51795

Explore proteomics data for CLCN5 at MOPED

Post-translational modifications: 

  • Ubiquitinated by NEDD4L in the presence of albumin; which promotes endocytosis and proteasomal degradation1
  • Ubiquitination2 at Lys579
  • Modification sites at PhosphoSitePlus

  • See CLCN5 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (5 alternative transcripts): 
    NP_000075.1  NP_001121370.1  NP_001121371.1  NP_001259031.1  NP_001269092.1  

    ENSEMBL proteins: 
     ENSP00000365256   ENSP00000365259   ENSP00000476732   ENSP00000365276   ENSP00000304257  
    Reactome Protein details: P51795

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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-5
    ClC family

    4 InterPro protein domains:
     IPR014743 Cl-channel_core
     IPR000644 CBS_dom
     IPR002247 Cl_channel-5
     IPR001807 Cl-channel_volt-gated

    Graphical View of Domain Structure for InterPro Entry P51795

    ProtoNet protein and cluster: P51795

    3 Blocks protein domains:
    IPB000644 CBS domain
    IPB001807 Chloride channel signature
    IPB002247 CLC-5 chloride channel signature


    UniProtKB/Swiss-Prot: CLCN5_HUMAN, P51795
    Similarity: Belongs to the chloride channel (TC 2.A.49) family. ClC-5/CLCN5 subfamily
    Similarity: Contains 2 CBS domains


    Find genes that share domains with CLCN5           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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: CLCN5_HUMAN, P51795
    Function: Proton-coupled chloride transporter. Functions as antiport system and exchanges chloride ions against
    protons. Important for normal acidification of the endosome lumen. May play an important role in renal tubular
    function

         Genatlas biochemistry entry for CLCN5:
    chloride voltage-gated channel 5,expressed in the epithelial cell lining the proximal tubules and the thick
    ascending limbs of Henle's loop,likely involved in the receptor-mediated endocytic pathway

         Gene Ontology (GO): Selected molecular function terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005216ion channel activity ----
    GO:0005247voltage-gated chloride channel activity IEA--
    GO:0005254chloride channel activity TAS8559248
    GO:0005524ATP binding IEA--
    GO:0015297antiporter activity IEA--
         
    Find genes that share ontologies with CLCN5           About GenesLikeMe


    Phenotypes:
         1 GenomeRNAi human phenotype for CLCN5:
     Decreased homologous recombina 

         8 MGI mutant phenotypes (inferred from 8 alleles(MGI details for Clcn5):
     cellular  craniofacial  homeostasis/metabolism  liver/biliary system  no phenotypic analysis 
     normal  renal/urinary system  skeleton 

    Find genes that share phenotypes with CLCN5           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for CLCN5: Clcn5tm1Gug Clcn5tm6.2Tjj

       genOway: Develop your customized and physiologically relevant rodent model for CLCN5

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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
    CLCN5_HUMAN, P51795: Golgi apparatus membrane; Multi-pass membrane protein. Endosome membrane; Multi-pass
    membrane protein. Cell membrane; Multi-pass membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    endosome5
    golgi apparatus5
    plasma membrane5
    endoplasmic reticulum1
    peroxisome1

    Gene Ontology (GO): Selected cellular component terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000139Golgi membrane IEA--
    GO:0005765lysosomal membrane IDA17897319
    GO:0005768endosome ----
    GO:0005887integral component of plasma membrane TAS8559248
    GO:0010008endosome membrane TAS--

    Find genes that share ontologies with CLCN5           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 CLCN5 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


    Find genes that share SuperPaths with CLCN5           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    5 Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for CLCN5
        Cholera Infection
    Hepatic ABC Transporters
    PKA Signaling
    cAMP Pathway
    Activation of cAMP-Dependent PKA

    1 Reactome Pathway for CLCN5
        Stimuli-sensing channels


        Pathway & Disease-focused RT2 Profiler PCR Array including CLCN5: 
              Neurotoxicity in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for CLCN5

    STRING Interaction Network Preview (showing 5 interactants - click image to see 9)

    Selected Interacting proteins for CLCN5 (P517953 ENSP000003652564) via UniProtKB, MINT, STRING, and/or I2D (see all 9)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CFL1P235283, ENSP000003096294I2D: score=1 STRING: ENSP00000309629
    WWP2O003083, ENSP000003482834I2D: score=1 STRING: ENSP00000348283
    MAGI1Q96QZ73, ENSP000003854504I2D: score=1 STRING: ENSP00000385450
    WWP1Q9H0M03, ENSP000002654284I2D: score=1 STRING: ENSP00000265428
    TMEM9BENSP000003118424STRING: ENSP00000311842
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006810transport TAS8559248
    GO:0006821chloride transport ----
    GO:0006897endocytosis IEA--
    GO:0007588excretion TAS8559248
    GO:0034220ion transmembrane transport TAS--

    Find genes that share ontologies with CLCN5           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 CLCN5

    1 HMDB Compound for CLCN5    About this table
    CompoundSynonyms CAS #PubMed Ids
    ChlorineCl2 (see all 13)16887-00-6--

    6 Novoseek inferred chemical compound relationships for CLCN5 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    chloride 85.8 90 16226913 (4), 9062355 (3), 9259268 (3), 10906159 (3) (see all 54)
    nppb 59.4 1 8613551 (1)
    calcium 27 11 15125028 (1), 16247550 (1), 15052463 (1), 9519207 (1) (see all 9)
    hydrogen 14.9 2 16034421 (1), 18184518 (1)
    creatinine 0 2 15125028 (1), 17162149 (1)
    h2o2 0 1 11350746 (1)



    Find genes that share compounds with CLCN5           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 CLCN5 gene (5 alternative transcripts): 
    NM_000084.4  NM_001127898.3  NM_001127899.3  NM_001272102.1  NM_001282163.1  

    Unigene Cluster for CLCN5:

    Chloride channel, voltage-sensitive 5
    Hs.166486  [show with all ESTs]
    Unigene Representative Sequence: NM_001127899
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000376088(uc004dor.1 uc004doq.1 uc004dos.1 uc004dot.1)
    ENST00000376091 ENST00000482218 ENST00000376108 ENST00000307367
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    Additional mRNA sequence: 

    AK021494.1 AK025562.1 AK056560.1 AK092049.1 AK290940.1 AK308089.1 BC051691.1 BC130429.1 
    BC130431.1 NR_073607.1 X81836.1 X91906.1 

    8 DOTS entries:

    DT.314531  DT.100750179  DT.121316336  DT.100018703  DT.425466  DT.205871  DT.100740812  DT.92011110 

    Selected AceView cDNA sequences (see all 168):

    CA412774 AW241642 AW207317 BM718051 AI222161 CK300866 AK056560 AA714782 
    BE221516 BE048779 AI493055 CK903120 BM723207 AA227146 AA441964 AA743724 
    AU186091 AI681893 AI831902 AI343688 BM838013 AW291578 AA328792 AK025562 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for CLCN5    About this scheme

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


    ECgene alternative splicing isoforms for CLCN5

    (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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    CLCN5 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    CLCN5 Expression
    About this image


    CLCN5 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 5) fully expand
     
     Kidney (Urinary System)
             Proximal Tubule Cells Proximal Tubule
     
     Epithelial Cells
             Proximal Tubule Cells Proximal Tubule
     
     Endothelium (Cardiovascular System)
             Mature Endothelial Cells Blood Brain Barrier
     
     Brain (Nervous System)
             Mature Endothelial Cells Blood Brain Barrier
     
     Liver (Hepatobiliary System)
    CLCN5 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    CLCN5 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.166486

    UniProtKB/Swiss-Prot: CLCN5_HUMAN, P51795
    Tissue specificity: Kidney. Moderately expressed in aortic vascular smooth muscle and endothelial cells, and at a
    slightly higher level in the coronary vascular smooth muscle

        Pathway & Disease-focused RT2 Profiler PCR Array including CLCN5: 
              Neurotoxicity 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 and fungi.

    Orthologs for CLCN5 gene from Selected species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Clcn51 , 5 chloride channel 51, 5 91.34(n)1
    97.18(a)1
      X (3.21 cM)5
    127281  NM_001243762.11  NP_001230691.11 
     71538105 
    chicken
    (Gallus gallus)
    Aves CLCN51 chloride channel 5 79.03(n)
    86.6(a)
      422285  XM_004940721.1  XP_004940778.1 
    lizard
    (Anolis carolinensis)
    Reptilia CLCN56
    chloride channel, voltage-sensitive 5
    83(a)
    1 ↔ 1
    GL343577.1(173104-208111)
    African clawed frog
    (Xenopus laevis)
    Amphibia LOC3978802 chloride channel ClC-5 77.68(n)    AF063904.1 
    zebrafish
    (Danio rerio)
    Actinopterygii si:dkey-22f5.81 si:dkey-22f5.8 72.81(n)
    80.22(a)
      562336  XM_001920748.3  XP_001920783.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG52843 chloride channel 59(a)   72D5   --
    worm
    (Caenorhabditis elegans)
    Secernentea clh-56
    Protein CLH-5 (clh-5) mRNA, complete cds
    50(a)
    1 → many
    II(9094680-9098846) WBGene00000532
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes GEF16
    Voltage-gated chloride channel localized to the go...
    31(a)
    1 → many
    X(507746-510085) YJR040W


    ENSEMBL Gene Tree for CLCN5 (if available)
    TreeFam Gene Tree for CLCN5 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for CLCN5 gene
    CLCN72  CLCN32  CLCN42  CLCN62  CLCNKB2  CLCNKA2  CLCN12  CLCN22  
    2 SIMAP similar genes for CLCN5 using alignment to 2 protein entries:     CLCN5_HUMAN (see all proteins):
    CLCN4    CLCN3

    Find genes that share paralogs with CLCN5           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 CLCN5 (see all 1869)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1442079671,2,,4
    C,FNephrolithiasis 2 (NPHL2)4 --49855363(+) TAGCAC/GTTCCA 19 T S mis11Minor allele frequency- G:0.00NA 4506
    VAR_0016184
    Hypophosphatemic rickets, X-linked recessive (XLRHR)4--see VAR_0016182 S L mis40--------
    VAR_0655934
    Nephrolithiasis 2 (NPHL2)4--see VAR_0655932 G A mis40--------
    VAR_0656044
    Nephrolithiasis 2 (NPHL2)4--see VAR_0656042 L F mis40--------
    VAR_0016204
    Nephrolithiasis 1 (NPHL1)4--see VAR_0016202 G E mis40--------
    VAR_0655944
    Nephrolithiasis 2 (NPHL2)4--see VAR_0655942 C R mis40--------
    VAR_0656054
    Nephrolithiasis 2 (NPHL2)4--see VAR_0656052 N K mis40--------
    VAR_0656144
    Nephrolithiasis 2 (NPHL2)4--see VAR_0656142 W G mis40--------
    VAR_0016214
    Nephrolithiasis 2 (NPHL2)4--see VAR_0016212 G R mis40--------
    VAR_0016234
    Nephrolithiasis 2 (NPHL2)4--see VAR_0016232 E D mis40--------

    HapMap Linkage Disequilibrium report for CLCN5 (49687225 - 49863892 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for CLCN5:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2740156CNV Deletion23290073
    esv2673611CNV Deletion23128226
    esv2740157CNV Deletion23290073
    nsv508770CNV Insertion20534489
    esv33289CNV Loss17666407

    Human Gene Mutation Database (HGMD): CLCN5
    Locus Specific Mutation Databases (LSDB): CLCN5

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing CLCN5
    DNA2.0 Custom Variant and Variant Library Synthesis for CLCN5

    (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: 300008   
    OMIM disorders: 300009  310468  300554  308990  
    UniProtKB/Swiss-Prot: CLCN5_HUMAN, P51795
  • Hypophosphatemic rickets, X-linked recessive (XLRHR) [MIM:300554]: A renal disease belonging to the 'Dent
    disease complex', a group of disorders characterized by proximal renal tubular defect, hypercalciuria,
    nephrocalcinosis, and renal insufficiency. The spectrum of phenotypic features is remarkably similar in the
    various disorders, except for differences in the severity of bone deformities and renal impairment. XLRH patients
    present with rickets or osteomalacia, hypophosphatemia due to decreased renal tubular phosphate reabsorption,
    hypercalciuria, and low molecular weight proteinuria. Patients develop nephrocalcinosis with progressive renal
    failure in adulthood. Female carriers may have asymptomatic hypercalciuria or hypophosphatemia only. Note=The
    disease is caused by mutations affecting the gene represented in this entry
  • Nephrolithiasis 2 (NPHL2) [MIM:300009]: An X-linked recessive renal disease belonging to the 'Dent
    disease complex', a group of disorders characterized by proximal renal tubular defect, hypercalciuria,
    nephrocalcinosis, and renal insufficiency. The spectrum of phenotypic features is remarkably similar in the
    various disorders, except for differences in the severity of bone deformities and renal impairment.
    Nephrolithiasis type 2 patients manifest hypercalciuria, hypophosphatemia, aminoaciduria, nephrocalcinosis and
    nephrolithiasis, renal insufficiency leading to renal failure in adulthood, rickets (33% of patients) and
    osteomalacia. Note=The disease is caused by mutations affecting the gene represented in this entry
  • Nephrolithiasis 1 (NPHL1) [MIM:310468]: An X-linked recessive renal disease belonging to the 'Dent
    disease complex', a group of disorders characterized by proximal renal tubular defect, hypercalciuria,
    nephrocalcinosis and renal insufficiency. The spectrum of phenotypic features is remarkably similar in the
    various disorders, except for differences in the severity of bone deformities and renal impairment.
    Nephrolithiasis type 1 presents with hypercalciuria, nephrocalcinosis, renal stones and renal insufficiency.
    Patients lack urinary acidification defects, rickets, and osteomalacia. Note=The disease is caused by mutations
    affecting the gene represented in this entry
  • Low molecular weight proteinuria with hypercalciuria and nephrocalcinosis (LMWPHN) [MIM:308990]: An
    X-linked renal disease belonging to the 'Dent disease complex', a group of disorders characterized by proximal
    renal tubular defect, hypercalciuria, nephrocalcinosis, and renal insufficiency. The spectrum of phenotypic
    features is remarkably similar in the various disorders, except for differences in the severity of bone
    deformities and renal impairment. LMWPHN is a slowly progressive disorder. Patients tend to have hypercalciuric
    nephrocalcinosis without rickets or renal failure. Note=The disease is caused by mutations affecting the gene
    represented in this entry

  • 12 diseases for CLCN5:    
    About MalaCards
    dent's disease    nephrolithiasis    dent disease 1    proteinuria, low molecular weight, with hypercalciuric nephrocalcinosis
    nephrolithiasis, type i    narcolepsy 7    x-linked hypophosphatemia    proteinuria
    nephrocalcinosis    root resorption    narcolepsy    aminoaciduria

    9 diseases from the University of Copenhagen DISEASES database for CLCN5:
    Nephrocalcinosis     Nephrolithiasis     Proteinuria     Fanconi syndrome
    Oculocerebrorenal syndrome     Rickets     X-linked hypophosphatemia     Kidney failure
    Hypophosphatemia

    Find genes that share disorders with CLCN5           About GenesLikeMe

    Selected Novoseek inferred disease relationships for CLCN5 gene (see all 17)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    dent disease 99.1 129 10916075 (4), 15086899 (4), 19546591 (4), 10469281 (3) (see all 65)
    renal tubular disorder 95.2 7 9062355 (2), 8559248 (2), 14521953 (1), 9931332 (1) (see all 5)
    nephrocalcinosis 94.1 15 15692680 (2), 9062355 (1), 9328929 (1), 14521953 (1) (see all 13)
    hypercalciuria 93.8 39 10620204 (5), 16807762 (4), 9596078 (2), 9931332 (2) (see all 20)
    nephrolithiasis 91.6 31 9259268 (2), 14673707 (2), 9187673 (1), 9596078 (1) (see all 26)
    proteinuria 83 37 16807762 (3), 9931332 (2), 11136179 (2), 10620205 (2) (see all 30)
    rickets 80.4 1 9187673 (1)
    aminoaciduria 79.7 1 9596078 (1)
    renal stone 77.5 7 9259268 (2), 14521953 (1), 8559248 (1), 11262581 (1) (see all 6)
    rickets hypophosphatemic 74.5 7 9452997 (2), 9596078 (2), 10720930 (1), 14673707 (1) (see all 5)

    Genetic Association Database (GAD): CLCN5
    Human Genome Epidemiology (HuGE) Navigator: CLCN5 (2 documents)

    Export disorders for CLCN5 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)
    About This Section

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    PubMed articles for CLCN5 gene, integrated from 10 sources (see all 159):
    (articles sorted by number of sources associating them with CLCN5)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Idiopathic low molecular weight proteinuria associated with hypercalciuric nephrocalcinosis in Japanese children is due to mutations of the renal chloride channel (CLCN5). (PubMed id 9062355)1, 2, 4, 9 Lloyd S.E.... Thakker R.V. (J. Clin. Invest. 1997)
    2. A common molecular basis for three inherited kidney stone diseases. (PubMed id 8559248)1, 2, 3, 9 Lloyd S.E.... Thakker R.V. (Nature 1996)
    3. X-linked recessive nephrolithiasis: presentation and diagnosis in children. (PubMed id 9602200)1, 2, 3, 9 Schurman S.J.... Scheinman S.J. (J. Pediatr. 1998)
    4. Isolation and partial characterization of a chloride channel gene which is expressed in kidney and is a candidate for Dent's disease (an X-linked hereditary nephrolithiasis). (PubMed id 7874126)1, 2, 3 Fisher S.... Craig I.W. (Hum. Mol. Genet. 1994)
    5. Four additional CLCN5 exons encode a widely expressed novel long CLC- 5 isoform but fail to explain Dent's phenotype in patients without mutations in the short variant. (PubMed id 12886045)1, 2, 9 Ludwig M.... Utsch B. (Kidney Blood Press. Res. 2003)
    6. Nedd4-2 functionally interacts with ClC-5: involvement in constitutive albumin endocytosis in proximal tubule cells. (PubMed id 15489223)1, 2, 9 Hryciw D.H.... Poronnik P. (J. Biol. Chem. 2004)
    7. A missense mutation in the chloride/proton ClC-5 antiporter gene results in increased expression of an alternative mRNA form that lacks exons 10 and 11. Identification of seven new CLCN5 mutations in patients with Dent's disease. (PubMed id 17262170)1, 2, 9 Ramos-Trujillo E.... Claverie-Martin F. (J. Hum. Genet. 2007)
    8. Characterisation of renal chloride channel, CLCN5, mutations in hypercalciuric nephrolithiasis (kidney stones) disorders. (PubMed id 9259268)1, 2, 9 Lloyd S.E.... Thakker R.V. (Hum. Mol. Genet. 1997)
    9. Evidence for genetic heterogeneity in Dent's disease. (PubMed id 15086899)1, 2, 9 Hoopes R.R. Jr....Scheinman S.J. (Kidney Int. 2004)
    10. De novo insertion of an Alu sequence in the coding region of the CLCN5 gene results in Dent's disease. (PubMed id 14569459)1, 4, 9 Claverie-Martin F....GarcA-a-Nieto V. (Hum. Genet. 2003)

    (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: 1184 HGNC: 2023 AceView: CLCN5 Ensembl:ENSG00000171365 euGenes: HUgn1184
    ECgene: CLCN5 H-InvDB: CLCN5

    (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 CLCN5 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=CLCN5[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 CLCN5 gene:
    Search GeneIP for patents involving CLCN5

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



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