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

Gene ID: 1184, updated on 2-Aug-2021

Summary

Official Symbol
CLCN5provided by HGNC
Official Full Name
chloride voltage-gated channel 5provided by HGNC
Primary source
HGNC:HGNC:2023
See related
Ensembl:ENSG00000171365 MIM:300008
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; DENT1; 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]
Expression
Biased expression in kidney (RPKM 20.4), liver (RPKM 3.6) and 13 other tissues See more
Orthologs
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Genomic context

See CLCN5 in Genome Data Viewer
Location:
Xp11.23
Exon count:
17
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (49922596..50099231)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (49687206..49863887)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ubiquitin specific peptidase 27 X-linked Neighboring gene CPSF1 pseudogene 2 Neighboring gene RNA, U6 small nuclear 421, pseudogene Neighboring gene microRNA 532 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 anchoring protein 4

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ11432

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
 
enables antiporter activity TAS
Traceable Author Statement
more info
 
enables chloride channel activity TAS
Traceable Author Statement
more info
PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables solute:proton antiporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables voltage-gated chloride channel activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
involved_in chloride transport IEA
Inferred from Electronic Annotation
more info
 
involved_in endocytosis IEA
Inferred from Electronic Annotation
more info
 
involved_in excretion TAS
Traceable Author Statement
more info
PubMed 
involved_in ion transmembrane transport TAS
Traceable Author Statement
more info
 
involved_in proton transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 
located_in Golgi membrane IEA
Inferred from Electronic Annotation
more info
 
located_in apical part of cell IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
is_active_in early endosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in endosome membrane TAS
Traceable Author Statement
more info
 
is_active_in integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in lysosomal membrane HDA PubMed 
located_in membrane HDA PubMed 
located_in membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 
is_active_in synaptic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
H(+)/Cl(-) exchange transporter 5
Names
chloride channel, voltage-sensitive 5
chloride transporter ClC-5
voltage-gated chloride ion channel CLCN5

NCBI Reference Sequences (RefSeq)

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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 RefSeqGene

    Range
    4981..181615
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    See identical proteins and their annotated locations for 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)
    AC231645, AK025562, AK290940, BC051691, BX950885
    Consensus CDS
    CCDS14328.1
    UniProtKB/Swiss-Prot
    P51795
    UniProtKB/TrEMBL
    A8K4H5
    Related
    ENSP00000365276.3, ENST00000376108.7
    Conserved Domains (2) summary
    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_001127898.4NP_001121370.1  H(+)/Cl(-) exchange transporter 5 isoform a

    See identical proteins and their annotated locations for 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)
    AC231645, AC236430, AK025562, AK056560, BC051691, DA652242
    Consensus CDS
    CCDS48115.1
    UniProtKB/Swiss-Prot
    P51795
    Related
    ENSP00000365259.3, ENST00000376091.8
    Conserved Domains (2) summary
    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:651801
    CBS_pair_voltage-gated_CLC_euk_bac; Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the voltage gated CLC (chloride channel) in eukaryotes and bacteria
  3. NM_001127899.4NP_001121371.1  H(+)/Cl(-) exchange transporter 5 isoform a

    See identical proteins and their annotated locations for 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)
    AC231645, AC236430, AK025562, AK092049, BC051691, BK000969, DA737534
    Consensus CDS
    CCDS48115.1
    UniProtKB/Swiss-Prot
    P51795
    UniProtKB/TrEMBL
    B3KRR2
    Related
    ENSP00000365256.3, ENST00000376088.7
    Conserved Domains (2) summary
    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:651801
    CBS_pair_voltage-gated_CLC_euk_bac; Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the voltage gated CLC (chloride channel) in eukaryotes and bacteria
  4. NM_001272102.2NP_001259031.1  H(+)/Cl(-) exchange transporter 5 isoform c

    See identical proteins and their annotated locations for NP_001259031.1

    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)
    AC236430, AK092049, BF513571
    Consensus CDS
    CCDS69763.1
    UniProtKB/TrEMBL
    B3KRR2, V9GYG7
    Related
    ENSP00000476732.1, ENST00000482218.2
  5. NM_001282163.2NP_001269092.1  H(+)/Cl(-) exchange transporter 5 isoform d

    See identical proteins and their annotated locations for 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)
    AC231645, AK025562, BC051691, X91906
    UniProtKB/Swiss-Prot
    P51795
    Conserved Domains (4) summary
    COG0517
    Location:603749
    CBS; CBS domain [Signal transduction mechanisms]
    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 ...
    pfam00654
    Location:169570
    Voltage_CLC; Voltage gated chloride channel

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    49922596..50099231
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017029258.1XP_016884747.1  H(+)/Cl(-) exchange transporter 5 isoform X1

  2. XM_017029257.1XP_016884746.1  H(+)/Cl(-) exchange transporter 5 isoform X1

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