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CLCN5 chloride channel, voltage-sensitive 5 [ Homo sapiens (human) ]

Gene ID: 1184, updated on 27-Sep-2014
Official Symbol
CLCN5provided by HGNC
Official Full Name
chloride channel, voltage-sensitive 5provided by HGNC
Primary source
HGNC:HGNC:2023
See related
Ensembl:ENSG00000171365; HPRD:02053; MIM:300008; Vega:OTTHUMG00000021514
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
XRN; CLC5; XLRH; CLCK2; ClC-5; DENTS; NPHL1; NPHL2; hCIC-K2
Summary
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]
See CLCN5 in Epigenomics, MapViewer
Location:
Xp11.23-p11.22
Exon count:
17
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) X NC_000023.11 (49922615..50099235)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (49687225..49863892)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ubiquitin specific peptidase 27, X-linked Neighboring gene cleavage and polyadenylation specific factor 1, 160kDa pseudogene Neighboring gene microRNA 188 Neighboring gene microRNA 500a Neighboring gene microRNA 500b Neighboring gene microRNA 362 Neighboring gene microRNA 501 Neighboring gene microRNA 660 Neighboring gene microRNA 502 Neighboring gene peptide YY, 3 (pseudogene) Neighboring gene A kinase (PRKA) anchor protein 4

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Dent disease 1
MedGen: C1848336 OMIM: 300009 GeneReviews: Dent Disease
Compare labs
Proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis
MedGen: C1839874 OMIM: 308990 GeneReviews: Not available
Compare labs
X-linked recessive hypophosphatemic rickets
MedGen: C1845168 OMIM: 300554 GeneReviews: Not available
Compare labs
X-linked recessive nephrolithiasis with renal failure
MedGen: C0403720 OMIM: 310468 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-10-18)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-10-18)

ClinGen Genome Curation PagePubMed
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • FLJ11432

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
antiporter activity IEA
Inferred from Electronic Annotation
more info
 
chloride channel activity TAS
Traceable Author Statement
more info
PubMed 
voltage-gated chloride channel activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
chloride transmembrane transport TAS
Traceable Author Statement
more info
PubMed 
endocytosis IEA
Inferred from Electronic Annotation
more info
 
excretion TAS
Traceable Author Statement
more info
PubMed 
ion transmembrane transport TAS
Traceable Author Statement
more info
 
regulation of anion transport IEA
Inferred from Electronic Annotation
more info
 
transmembrane transport TAS
Traceable Author Statement
more info
 
transport TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
Golgi membrane IEA
Inferred from Electronic Annotation
more info
 
apical part of cell IDA
Inferred from Direct Assay
more info
PubMed 
endosome membrane TAS
Traceable Author Statement
more info
 
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
lysosomal membrane IDA
Inferred from Direct Assay
more info
PubMed 
membrane IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
H(+)/Cl(-) exchange transporter 5
Names
H(+)/Cl(-) exchange transporter 5
chloride transporter ClC-5
voltage-gated chloride ion channel CLCN5

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_007159.3 

    Range
    5000..181620
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000084.4NP_000075.1  H(+)/Cl(-) exchange transporter 5 isoform b

    See proteins identical to NP_000075.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3, also known as type 3) lacks several 5' exons but has an alternate 5' exon, and it thus differs in the 5' UTR and uses a downstream start codon, compared to variant 1. The resulting isoform (b) has a shorter N-terminus, compared to isoform a.
    Source sequence(s)
    AA743724, AC231645, AK025562, AK290940, BC051691, BX950885
    Consensus CDS
    CCDS14328.1
    UniProtKB/TrEMBL
    A8K4H5
    UniProtKB/Swiss-Prot
    P51795
    Conserved Domains (3) summary
    COG0517
    Location:583729
    COG0517; FOG: CBS domain [General function prediction only]
    cd03684
    Location:72570
    ClC_3_like; ClC-3-like chloride channel proteins. This CD includes ClC-3, ClC-4, ClC-5 and ClC-Y1. ClC-3 was initially cloned from rat kidney. Expression of ClC-3 produces outwardly-rectifying Cl currents that are inhibited by protein kinase C activation. It has ...
    cd04591
    Location:595731
    CBS_pair_EriC_assoc_euk_bac; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in eukaryotes and bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of ...
  2. NM_001127898.3NP_001121370.1  H(+)/Cl(-) exchange transporter 5 isoform a

    See proteins identical to NP_001121370.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2, also known as type 1) uses an alternate splice site in the 5' UTR, compared to variant 1. Both variants 1 and 2 encode the same isoform (a).
    Source sequence(s)
    AA743724, AC231645, AK025562, AK056560, BC051691, DA652242
    Consensus CDS
    CCDS48115.1
    UniProtKB/Swiss-Prot
    P51795
    Conserved Domains (3) summary
    COG0517
    Location:653799
    COG0517; FOG: CBS domain [General function prediction only]
    cd03684
    Location:142640
    ClC_3_like; ClC-3-like chloride channel proteins. This CD includes ClC-3, ClC-4, ClC-5 and ClC-Y1. ClC-3 was initially cloned from rat kidney. Expression of ClC-3 produces outwardly-rectifying Cl currents that are inhibited by protein kinase C activation. It has ...
    cd04591
    Location:665801
    CBS_pair_EriC_assoc_euk_bac; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in eukaryotes and bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of ...
  3. NM_001127899.3NP_001121371.1  H(+)/Cl(-) exchange transporter 5 isoform a

    See proteins identical to NP_001121371.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1, also known as type 2) represents the longest transcript and encodes the longest isoform (a). Both variants 1 and 2 encode the same isoform.
    Source sequence(s)
    AA743724, AC231645, AK025562, AK092049, BC051691, BK000969, DA737534
    Consensus CDS
    CCDS48115.1
    UniProtKB/TrEMBL
    B3KRR2
    UniProtKB/Swiss-Prot
    P51795
    Related
    ENSP00000365256, OTTHUMP00000023279, ENST00000376088, OTTHUMT00000056542
    Conserved Domains (3) summary
    COG0517
    Location:653799
    COG0517; FOG: CBS domain [General function prediction only]
    cd03684
    Location:142640
    ClC_3_like; ClC-3-like chloride channel proteins. This CD includes ClC-3, ClC-4, ClC-5 and ClC-Y1. ClC-3 was initially cloned from rat kidney. Expression of ClC-3 produces outwardly-rectifying Cl currents that are inhibited by protein kinase C activation. It has ...
    cd04591
    Location:665801
    CBS_pair_EriC_assoc_euk_bac; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in eukaryotes and bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of ...
  4. NM_001272102.1NP_001259031.1  H(+)/Cl(-) exchange transporter 5 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate splice site in the 5' UTR, it lacks several 3' exons but has an alternate 3' terminal exon, and it thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (c) has a distinct and shorter C-terminus, compared to isoform a.
    Source sequence(s)
    AK092049, BF513571
    Consensus CDS
    CCDS69763.1
    UniProtKB/TrEMBL
    B3KRR2
    UniProtKB/TrEMBL
    V9GYG7
  5. NM_001282163.1NP_001269092.1  H(+)/Cl(-) exchange transporter 5 isoform d

    See proteins identical to NP_001269092.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4, also known as type 4) lacks several 5' exons but has an alternate 5' exon, and it thus differs in the 5' UTR and uses an alternate start codon, compared to variant 1. The resulting isoform (d) has a shorter and distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AA743724, AC231645, AK025562, BC051691, X91906
    UniProtKB/Swiss-Prot
    P51795
    Conserved Domains (3) summary
    COG0517
    Location:603749
    COG0517; FOG: CBS domain [General function prediction only]
    cd03684
    Location:92590
    ClC_3_like; ClC-3-like chloride channel proteins. This CD includes ClC-3, ClC-4, ClC-5 and ClC-Y1. ClC-3 was initially cloned from rat kidney. Expression of ClC-3 produces outwardly-rectifying Cl currents that are inhibited by protein kinase C activation. It has ...
    cd04591
    Location:615751
    CBS_pair_EriC_assoc_euk_bac; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in eukaryotes and bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000023.11 

    Range
    49922615..50099235
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

  1. AC_000155.1 

    Range
    47156646..47337277
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018934.2 

    Range
    49766989..49943526
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)