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CLCN6 chloride voltage-gated channel 6 [ Homo sapiens (human) ]

Gene ID: 1185, updated on 2-Oct-2018

Summary

Official Symbol
CLCN6provided by HGNC
Official Full Name
chloride voltage-gated channel 6provided by HGNC
Primary source
HGNC:HGNC:2024
See related
Ensembl:ENSG00000011021 MIM:602726; Vega:OTTHUMG00000002299
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
CLC-6
Summary
This gene encodes a member of the voltage-dependent chloride channel protein family. Members of this family can function as either chloride channels or antiporters. This protein is primarily localized to late endosomes and functions as a chloride/proton antiporter. Alternate splicing results in both coding and non-coding variants. Additional alternately spliced variants have been described but their full-length structure is unknown. [provided by RefSeq, Mar 2012]
Expression
Ubiquitous expression in brain (RPKM 13.0), testis (RPKM 10.2) and 24 other tissues See more
Orthologs

Genomic context

See CLCN6 in Genome Data Viewer
Location:
1p36.22
Exon count:
23
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (11806096..11843144)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (11866153..11903201)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene atrophin-1-like Neighboring gene chromosome 1 open reading frame 167 Neighboring gene uncharacterized LOC102724659 Neighboring gene methylenetetrahydrofolate reductase Neighboring gene NPPA antisense RNA 1 Neighboring gene natriuretic peptide A Neighboring gene natriuretic peptide B

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association analysis and fine mapping of NT-proBNP level provide novel insight into the role of the MTHFR-CLCN6-NPPA-NPPB gene cluster.
NHGRI GWA Catalog
Genome-wide association study identifies eight loci associated with blood pressure.
NHGRI GWA Catalog

Pathways from BioSystems

  • Disease, organism-specific biosystem (from REACTOME)
    Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
  • Diseases of signal transduction, organism-specific biosystem (from REACTOME)
    Diseases of signal transduction, organism-specific biosystemSignaling processes are central to human physiology (e.g., Pires-da Silva & Sommer 2003), and their disruption by either germ-line and somatic mutation can lead to serious disease. Here, the molecula...
  • Ion channel transport, organism-specific biosystem (from REACTOME)
    Ion channel transport, organism-specific biosystemIon channels mediate the flow of ions across the plasma membrane of cells. They are integral membrane proteins, typically a multimer of proteins, which, when arranged in the membrane, create a pore f...
  • Oncogenic MAPK signaling, organism-specific biosystem (from REACTOME)
    Oncogenic MAPK signaling, organism-specific biosystemThe importance of the RAS/RAF/MAPK cascade in regulating cellular proliferation, differentiation and survival is highlighted by the fact that components of the pathway are mutated with high frequency...
  • Signaling by BRAF and RAF fusions, organism-specific biosystem (from REACTOME)
    Signaling by BRAF and RAF fusions, organism-specific biosystemIn addition to the more prevalent point mutations, BRAF and RAF1 are also subject to activation as a result of translocation events that yield truncated or fusion products (Jones et al, 2008; Cin et ...
  • Stimuli-sensing channels, organism-specific biosystem (from REACTOME)
    Stimuli-sensing channels, organism-specific biosystemIon channels that mediate sensations such as pain, warmth, cold, taste pressure and vision. Channels that mediate these sensations include acid-sensing ion channels (ASICs) (Wang & Xu 2011, Qadri et ...
  • Transmembrane transport of small molecules, organism-specific biosystem (from REACTOME)
    Transmembrane transport of small molecules, organism-specific biosystem
    Transmembrane transport of small molecules

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0046

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
antiporter activity TAS
Traceable Author Statement
more info
 
protein binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
voltage-gated chloride channel activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
voltage-gated chloride channel activity NAS
Non-traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
cell volume homeostasis NAS
Non-traceable Author Statement
more info
PubMed 
chloride transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chloride transport NAS
Non-traceable Author Statement
more info
PubMed 
ion transmembrane transport TAS
Traceable Author Statement
more info
 
response to mechanical stimulus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
signal transduction NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
endosome membrane TAS
Traceable Author Statement
more info
 
integral component of membrane NAS
Non-traceable Author Statement
more info
PubMed 
lysosomal membrane HDA PubMed 

General protein information

Preferred Names
chloride transport protein 6
Names
chloride channel, voltage-sensitive 6

NCBI Reference Sequences (RefSeq)

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_008766.1 RefSeqGene

    Range
    4947..41995
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001256959.1NP_001243888.1  chloride transport protein 6 isoform 2

    See identical proteins and their annotated locations for NP_001243888.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AK294764, AL021155, DA229615, R20538
    Consensus CDS
    CCDS57972.1
    UniProtKB/Swiss-Prot
    P51797
    Related
    ENSP00000308367.7, ENST00000312413.10
    Conserved Domains (5) summary
    smart00116
    Location:586633
    CBS; Domain in cystathionine beta-synthase and other proteins
    COG0517
    Location:781831
    CBS; CBS domain [Signal transduction mechanisms]
    cd03685
    Location:40566
    ClC_6_like; ClC-6-like chloride channel proteins. This CD includes ClC-6, ClC-7 and ClC-B, C, D in plants. Proteins in this family are ubiquitous in eukarotes and their functions are unclear. They are expressed in intracellular organelles membranes. This family ...
    cd04591
    Location:679831
    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:118548
    Voltage_CLC; Voltage gated chloride channel
  2. NM_001286.3NP_001277.1  chloride transport protein 6 isoform 1

    See identical proteins and their annotated locations for NP_001277.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) is the longest transcript and encodes the longer isoform (1). This isoform is also known as CLC-6a.
    Source sequence(s)
    AL021155, D28475, DA229615, R20538
    Consensus CDS
    CCDS138.1
    UniProtKB/Swiss-Prot
    P51797
    Related
    ENSP00000234488.9, OTTHUMP00000002410, ENST00000346436.10, OTTHUMT00000006639
    Conserved Domains (3) summary
    smart00116
    Location:608655
    CBS; Domain in cystathionine beta-synthase and other proteins
    cd03685
    Location:49588
    ClC_6_like; ClC-6-like chloride channel proteins. This CD includes ClC-6, ClC-7 and ClC-B, C, D in plants. Proteins in this family are ubiquitous in eukarotes and their functions are unclear. They are expressed in intracellular organelles membranes. This family ...
    cd04591
    Location:701853
    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 ...

RNA

  1. NR_046428.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL021155, BC143844, D28475, DA229615, R20538

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    11806096..11843144
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_021735.2: Suppressed sequence

    Description
    NM_021735.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
  2. NM_021736.2: Suppressed sequence

    Description
    NM_021736.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
  3. NM_021737.2: Suppressed sequence

    Description
    NM_021737.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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