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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

CLCN5 Gene

protein-coding   GIFtS: 64
GCID: GC0XP049687

Chloride Channel, Voltage-Sensitive 5

(Previous names: nephrolithiasis 2, X-linked, nephrolithiasis 1 (X-linked),...)
(Previous symbols: NPHL2, NPHL1)
Microbiology & Infectious Diseases Congress
  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)
About This Section

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, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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, and among its related super-pathways are Activation of cAMP-Dependent PKA and Stimuli-sensing channels. 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000023.10  NC_018934.2  NT_086939.3  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for CLCN5

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

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
Subcellular location: Golgi apparatus membrane; Multi-pass membrane protein. Endosome membrane; Multi-pass
membrane protein. Cell membrane; Multi-pass membrane protein
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:

  • UniProtKB: Ubiquitinated by NEDD4L in the presence of albumin; which promotes endocytosis and proteasomal degradation
  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_P51795

  • CLCN5 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    CLCN5 Protein Expression
    REFSEQ proteins (5 alternative transcripts): 
    NP_000075.1  NP_001121370.1  NP_001121371.1  NP_001259031.1  NP_001269092.1  

    ENSEMBL proteins: 
     ENSP00000365256   ENSP00000365259   ENSP00000365276   ENSP00000304257  
    Reactome Protein details: P51795
    Human Recombinant Protein Products for CLCN5: 
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    Gene Ontology (GO): 5/7 cellular component terms (GO ID links to tree view) (see all 7):    About this table

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

    CLCN5 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    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 Cysta_beta_synth_core
     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


    CLCN5 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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    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): 5/6 molecular function terms (GO ID links to tree view) (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--
         
    CLCN5 for ontologies           About GeneDecksing


    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 

    CLCN5 for phenotypes           About GeneDecksing

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

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    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section

    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 transport0.49
    Stimuli-sensing channels0.49
    3SLC-mediated transmembrane transport
    Transmembrane transport of small molecules0.50
    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 QIAGEN Pathway Central Maps for CLCN5
        Cholera Infection
    Hepatic ABC Transporters
    PKA Signaling
    cAMP Pathway
    Activation of cAMP-Dependent PKA

    3        Reactome Pathways for CLCN5
        Transmembrane transport of small molecules
    Stimuli-sensing channels
    Ion channel transport



    CLCN5 for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for CLCN5

    STRING Interaction Network Preview (showing 5 interactants - click image to see 7)

    5/7 Interacting proteins for CLCN5 (P517953 ENSP000003652564) via UniProtKB, MINT, STRING, and/or I2D (see all 7)
    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
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

    Gene Ontology (GO): 5/6 biological process terms (GO ID links to tree view) (see all 6):    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--

    CLCN5 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    CLCN5 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
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    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)

    Search CenterWatch for drugs/clinical trials and news about CLCN5

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    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
    Congresses - knowledge worth sharing:  
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

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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 

    24/168 AceView cDNA sequences (see all 168):

    AI364970 BP351387 AL698104 BE048779 AA328792 BQ053833 AW614149 AW207317 
    BM674660 AW197209 AI222161 AA441964 BX496111 BF512717 BE221516 BQ773802 
    AU186091 AK092049 BM973024 AI681893 BM718051 AI240929 BE465487 AA227146 

    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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    CLCN5 expression in normal human tissues (normalized intensities)      CLCN5 embryonic expression: see
    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 
     5/6 selected tissues (see all 6) fully expand
     
     Kidney (Urinary System)
             Proximal Tubule Cells Proximal Tubule
     
     Blood Brain Barrier (Nervous System)
             Postnatal Endothelial Cells Blood Brain Barrier
     
     Pancreas (Endocrine System)
             Posterior foregut-like cells ( A scalable, suspension protocol for derivation of...
     
     Endothelium (Cardiovascular System)
             Postnatal Endothelial Cells Blood Brain Barrier
     
     Brain (Nervous System)
             Postnatal Endothelial Cells Blood Brain Barrier

    See CLCN5 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for CLCN5

    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

        SABiosciences Expression via Pathway-Focused PCR Array including CLCN5: 
              Neurotoxicity in human mouse rat

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    In Situ
    Assay Products:
     

     
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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)
    About This Section

    This gene was present in the common ancestor of animals and fungi.

    Orthologs for CLCN5 gene from 8/20 species (see all 20)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Clcn51 , 5 chloride channel 51, 5 91.3(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 79.28(n)
    86.85(a)
      422285  XM_420265.2  XP_420265.2 
    lizard
    (Anolis carolinensis)
    Reptilia CLCN56
    Uncharacterized protein
    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 LOC5623361 H(+)/Cl(-) exchange transporter 5-like 72.76(n)
    80.22(a)
      562336  XM_001920748.2  XP_001920783.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG52843 chloride channel 59(a)   72D5   --
    worm
    (Caenorhabditis elegans)
    Secernentea clh-56
    Protein CLH-5
    49(a)
    1 → many
    II(9094680-9098846)
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes GEF11 Gef1p 46.51(n)
    36.25(a)
      853497   NP_012574.1 


    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)
    About This Section
    Paralogs for CLCN5 gene
    CLCN72  CLCN32  CLCN42  CLCN62  CLCNKB2  CLCNKA2  CLCN22  CLCN12  
    2 SIMAP similar genes for CLCN5 using alignment to 1 protein entry:     CLCN5_HUMAN:
    CLCN4    CLCN3

    CLCN5 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/1869 SNPs in CLCN5 are shown (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
    ----------
    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--------
    VAR_0655964
    Nephrolithiasis 2 (NPHL2)4--see VAR_0655962 L P 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
    SABiosciences Cancer Mutation 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, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    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

  • 20/30 diseases for CLCN5 (see all 30):    About MalaCards
    dent's disease    nephrolithiasis    dent disease 1    proteinuria, low molecular weight, with hypercalciuric nephrocalcinosis
    nephrolithiasis, type i    x-linked hypophosphatemia    proteinuria    nephrocalcinosis
    focal glomerulosclerosis    aminoaciduria    oculocerebrorenal syndrome    root resorption
    rickets    fanconi syndrome    hypophosphatemia    bartter disease
    primary hyperoxaluria    osteomalacia    renal tubular acidosis    growth hormone deficiency

    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

    CLCN5 for disorders           About GeneDecksing

    10/17 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

    PubMed articles for CLCN5 gene, integrated from 9 sources (see all 158):
    (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. (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. (1996)
    3. X-linked recessive nephrolithiasis: presentation and diagnosis in children. (PubMed id 9602200)1, 2, 3, 9 Schurman S.J.... Scheinman S.J. (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. (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. (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. (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. (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. (1997)
    9. Evidence for genetic heterogeneity in Dent's disease. (PubMed id 15086899)1, 2, 9 Hoopes R.R....Scheinman S.J. (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....Garcia-Nieto V. (2003)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 1184 HGNC: 2023 AceView: CLCN5 Ensembl:ENSG00000171365 euGenes: HUgn1184
    ECgene: CLCN5 H-InvDB: CLCN5

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for CLCN5 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/CLCN5

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