Free for academic non-profit institutions. Other users need a Commercial license

Aliases for CLCN5 Gene

Aliases for CLCN5 Gene

  • Chloride Channel, Voltage-Sensitive 5 2 3
  • CLCK2 3 4 6
  • Chloride Transporter ClC-5 3 4
  • DENTS 3 6
  • NPHL1 3 6
  • NPHL2 3 6
  • ClC-5 3 4
  • Voltage-Gated Chloride Ion Channel CLCN5 3
  • H(+)/Cl(-) Exchange Transporter 5 3
  • Nephrolithiasis 1 (X-Linked) 2
  • Nephrolithiasis 2, X-Linked 2
  • Chloride Channel Protein 5 4
  • Chloride Channel 5 2
  • Dent Disease 2
  • HCIC-K2 3
  • CLC5 3
  • XLRH 3
  • XRN 3

External Ids for CLCN5 Gene

Previous Symbols for CLCN5 Gene

  • NPHL2
  • NPHL1

Summaries for CLCN5 Gene

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 hypophosphatemic rickets and nephrolithiasis. Among its related pathways are Activation of cAMP-Dependent PKA and Activation of cAMP-Dependent PKA. GO annotations related to this gene include chloride channel activity and antiporter activity. An important paralog of this gene is CLCN7.

UniProtKB/Swiss-Prot for CLCN5 Gene

  • 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

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLCN5 Gene

Genomics for CLCN5 Gene

Genomic Location for CLCN5 Gene

Start:
49,922,615 bp from pter
End:
50,099,235 bp from pter
Size:
176,621 bases
Orientation:
Plus strand

Genomic View for CLCN5 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for CLCN5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLCN5 Gene

Regulatory Elements for CLCN5 Gene

Proteins for CLCN5 Gene

  • Protein details for CLCN5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P51795-CLCN5_HUMAN
    Recommended name:
    H(+)/Cl(-) exchange transporter 5
    Protein Accession:
    P51795
    Secondary Accessions:
    • A1L475
    • B3KPN6
    • Q5JQD5
    • Q7RTN8

    Protein attributes for CLCN5 Gene

    Size:
    746 amino acids
    Molecular mass:
    83147 Da
    Quaternary structure:
    • 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

    Three dimensional structures from OCA and Proteopedia for CLCN5 Gene

    Alternative splice isoforms for CLCN5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CLCN5 Gene

Proteomics data for CLCN5 Gene at MOPED

Post-translational modifications for CLCN5 Gene

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

Other Protein References for CLCN5 Gene

No data available for DME Specific Peptides for CLCN5 Gene

Domains for CLCN5 Gene

Gene Families for CLCN5 Gene

HGNC:
  • CLCN :Ion channels / Chloride channels : Voltage-sensitive
IUPHAR :

UniProtKB/Swiss-Prot:

CLCN5_HUMAN
Domain:
  • Contains 2 CBS domains.:
    • P51795
Family:
  • Belongs to the chloride channel (TC 2.A.49) family. ClC-5/CLCN5 subfamily.:
    • P51795
genes like me logo Genes that share domains with CLCN5: view

Function for CLCN5 Gene

Molecular function for CLCN5 Gene

GENATLAS Biochemistry: chloride voltage-gated channel 5,expressed in the epithelial cell lining the proximal tubules and the thick ascending limbs of Henles loop,likely involved in the receptor-mediated endocytic pathway
UniProtKB/Swiss-Prot 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 Ontology (GO) - Molecular Function for CLCN5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005216 ion channel activity --
GO:0005247 voltage-gated chloride channel activity IEA --
GO:0005254 chloride channel activity TAS 8559248
GO:0005524 ATP binding IEA --
GO:0015297 antiporter activity IEA --
genes like me logo Genes that share ontologies with CLCN5: view
genes like me logo Genes that share phenotypes with CLCN5: view

Animal Models for CLCN5 Gene

MGI Knock Outs for CLCN5:

miRNA for CLCN5 Gene

miRTarBase miRNAs that target CLCN5

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for CLCN5 Gene

Localization for CLCN5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLCN5 Gene

Golgi apparatus membrane; Multi-pass membrane protein. Endosome membrane; Multi-pass membrane protein. Cell membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for CLCN5 Gene COMPARTMENTS Subcellular localization image for CLCN5 gene
Compartment Confidence
endosome 5
golgi apparatus 5
plasma membrane 5
endoplasmic reticulum 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for CLCN5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005765 lysosomal membrane IDA 17897319
GO:0005768 endosome --
GO:0005794 Golgi apparatus --
GO:0005887 integral component of plasma membrane TAS 8559248
genes like me logo Genes that share ontologies with CLCN5: view

Pathways for CLCN5 Gene

genes like me logo Genes that share pathways with CLCN5: view

Gene Ontology (GO) - Biological Process for CLCN5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport TAS 8559248
GO:0006821 chloride transport --
GO:0006897 endocytosis IEA --
GO:0007588 excretion TAS 8559248
GO:0034220 ion transmembrane transport TAS --
genes like me logo Genes that share ontologies with CLCN5: view

Compounds for CLCN5 Gene

(1) HMDB Compounds for CLCN5 Gene

Compound Synonyms Cas Number PubMed IDs
Chlorine
  • Cl2
16887-00-6

(6) Novoseek inferred chemical compound relationships for CLCN5 Gene

Compound -log(P) Hits PubMed IDs
chloride 85.8 77
nppb 59.4 1
calcium 27 9
hydrogen 14.9 2
creatinine 0 2
genes like me logo Genes that share compounds with CLCN5: view

Transcripts for CLCN5 Gene

Unigene Clusters for CLCN5 Gene

Chloride channel, voltage-sensitive 5:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for CLCN5 Gene

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

Relevant External Links for CLCN5 Gene

GeneLoc Exon Structure for
CLCN5
ECgene alternative splicing isoforms for
CLCN5

Expression for CLCN5 Gene

mRNA expression in normal human tissues for CLCN5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLCN5 Gene

This gene is overexpressed in Kidney - Cortex (4.8).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for CLCN5 Gene

SOURCE GeneReport for Unigene cluster for CLCN5 Gene Hs.166486

mRNA Expression by UniProt/SwissProt for CLCN5 Gene

P51795-CLCN5_HUMAN
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.
genes like me logo Genes that share expressions with CLCN5: view

Orthologs for CLCN5 Gene

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

Orthologs for CLCN5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CLCN5 36
  • 97.3 (n)
  • 97.3 (a)
CLCN5 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CLCN5 36
  • 93.38 (n)
  • 96.69 (a)
CLCN5 37
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CLCN5 36
  • 93.38 (n)
  • 97.79 (a)
CLCN5 37
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Clcn5 36
  • 91.34 (n)
  • 97.18 (a)
Clcn5 16
Clcn5 37
  • 97 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CLCN5 37
  • 76 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CLCN5 37
  • 90 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Clcn5 36
  • 91.6 (n)
  • 98.12 (a)
chicken
(Gallus gallus)
Aves CLCN5 36
  • 79.03 (n)
  • 86.6 (a)
CLCN5 37
  • 87 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CLCN5 37
  • 83 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia LOC397880 36
tropical clawed frog
(Silurana tropicalis)
Amphibia clcn5 36
  • 73.03 (n)
  • 82.9 (a)
Str.16383 36
zebrafish
(Danio rerio)
Actinopterygii clcn5 37
  • 76 (a)
OneToMany
CLCN5 (1 of 2) 37
  • 79 (a)
OneToMany
si:dkey-22f5.8 36
  • 72.81 (n)
  • 80.22 (a)
fruit fly
(Drosophila melanogaster)
Insecta ClC-c 37
  • 54 (a)
OneToMany
CG5284 38
  • 59 (a)
worm
(Caenorhabditis elegans)
Secernentea clh-5 37
  • 50 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GEF1 37
  • 31 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 58 (a)
OneToMany
Species with no ortholog for CLCN5:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for CLCN5 Gene

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

Paralogs for CLCN5 Gene

Paralogs for CLCN5 Gene

Selected SIMAP similar genes for CLCN5 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with CLCN5: view

Variants for CLCN5 Gene

Sequence variations from dbSNP and Humsavar for CLCN5 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type MAF
rs149257 -- 49,929,466(+) CCCTA(A/G)AGACG intron-variant
rs151259 -- 49,933,044(+) CCACT(A/G)TCACC intron-variant
rs151263 -- 50,005,282(+) gagca(A/G)aacta intron-variant
rs151265 -- 49,923,007(+) GGCGT(A/C/G/T)TTCCC intron-variant
rs151266 -- 49,924,472(+) AATAT(C/T)TTTGC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CLCN5 Gene

Variant ID Type Subtype PubMed ID
esv33289 CNV Loss 17666407
esv2673611 CNV Deletion 23128226
nsv508770 CNV Insertion 20534489
esv2740156 CNV Deletion 23290073
esv2740157 CNV Deletion 23290073

Relevant External Links for CLCN5 Gene

HapMap Linkage Disequilibrium report
CLCN5
Human Gene Mutation Database (HGMD)
CLCN5
Locus Specific Mutation Databases (LSDB)
CLCN5

Disorders for CLCN5 Gene

(4) OMIM Diseases for CLCN5 Gene (300008)

UniProtKB/Swiss-Prot

CLCN5_HUMAN
  • 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. {ECO:0000269 PubMed:8559248}. 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. {ECO:0000269 PubMed:15086899, ECO:0000269 PubMed:16247550, ECO:0000269 PubMed:16416111, ECO:0000269 PubMed:16822791, ECO:0000269 PubMed:17262170, ECO:0000269 PubMed:19657328, ECO:0000269 PubMed:8559248, ECO:0000269 PubMed:9187673, ECO:0000269 PubMed:9259268, ECO:0000269 PubMed:9602200, ECO:0000269 PubMed:9853249}. 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. {ECO:0000269 PubMed:8559248}. 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. {ECO:0000269 PubMed:11136179, ECO:0000269 PubMed:9062355}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(17) Novoseek inferred disease relationships for CLCN5 Gene

Disease -log(P) Hits PubMed IDs
dent disease 99.1 118
renal tubular disorder 95.2 7
nephrocalcinosis 94.1 14
hypercalciuria 93.8 29
nephrolithiasis 91.6 28

Relevant External Links for CLCN5

Genetic Association Database (GAD)
CLCN5
Human Genome Epidemiology (HuGE) Navigator
CLCN5
genes like me logo Genes that share disorders with CLCN5: view

Publications for CLCN5 Gene

  1. Idiopathic low molecular weight proteinuria associated with hypercalciuric nephrocalcinosis in Japanese children is due to mutations of the renal chloride channel (CLCN5). (PMID: 9062355) Lloyd S.E. … Thakker R.V. (J. Clin. Invest. 1997) 3 4 23 49
  2. A common molecular basis for three inherited kidney stone diseases. (PMID: 8559248) Lloyd S.E. … Thakker R.V. (Nature 1996) 2 3 4 23
  3. X-linked recessive nephrolithiasis: presentation and diagnosis in children. (PMID: 9602200) Schurman S.J. … Scheinman S.J. (J. Pediatr. 1998) 2 3 4 23
  4. Cloning and characterization of CLCN5, the human kidney chloride channel gene implicated in Dent disease (an X-linked hereditary nephrolithiasis). (PMID: 8575751) Fisher S.E. … Craig I.W. (Genomics 1995) 3 4 23
  5. A second family with XLRH displays the mutation S244L in the CLCN5 gene. (PMID: 9187673) Oudet C. … Hanauer A. (Hum. Genet. 1997) 3 4 23

Products for CLCN5 Gene

Sources for CLCN5 Gene

Back to Top

Content