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

Aliases for CLCN6 Gene

Aliases for CLCN6 Gene

  • Chloride Channel, Voltage-Sensitive 6 2 3
  • CLC-6 3 4
  • Chloride Transport Protein 6 3
  • Chloride Channel Protein 6 4
  • Chloride Channel 6 2
  • KIAA0046 4

External Ids for CLCN6 Gene

Previous GeneCards Identifiers for CLCN6 Gene

  • GC01P011939
  • GC01P011711
  • GC01P011475
  • GC01P011575
  • GC01P011800
  • GC01P011866
  • GC01P011021

Summaries for CLCN6 Gene

Entrez Gene Summary for CLCN6 Gene

  • 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]

GeneCards Summary for CLCN6 Gene

CLCN6 (Chloride Channel, Voltage-Sensitive 6) is a Protein Coding gene. Among its related pathways are Activation of cAMP-Dependent PKA and Activation of cAMP-Dependent PKA. GO annotations related to this gene include voltage-gated chloride channel activity and antiporter activity. An important paralog of this gene is CLCN7.

UniProtKB/Swiss-Prot for CLCN6 Gene

  • Chloride transport protein, initially identified as voltage-gated chloride channel. The presence of the conserved gating glutamate residues suggests that is functions as antiporter

Gene Wiki entry for CLCN6 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLCN6 Gene

Genomics for CLCN6 Gene

Regulatory Elements for CLCN6 Gene

Transcription factor binding sites by QIAGEN in the CLCN6 gene promoter:

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for CLCN6 Gene

11,806,096 bp from pter
11,843,144 bp from pter
37,049 bases
Plus strand

Genomic View for CLCN6 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for CLCN6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLCN6 Gene

Proteins for CLCN6 Gene

  • Protein details for CLCN6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Chloride transport protein 6
    Protein Accession:
    Secondary Accessions:
    • A8K1T4
    • B4DGT7
    • F8W9R3
    • O60818
    • O60819
    • O60820
    • O60821
    • P78520
    • P78521
    • Q17R81
    • Q5SNW2
    • Q5SNW3
    • Q5SNX1
    • Q5SNX2
    • Q5SNX3
    • Q99427
    • Q99428
    • Q99429

    Protein attributes for CLCN6 Gene

    869 amino acids
    Molecular mass:
    97289 Da
    Quaternary structure:
    No Data Available
    • The CLC channel family contains both chloride channels and proton-coupled anion transporters that exchange chloride or another anion for protons. The presence of conserved gating glutamate residues is typical for family members that function as antiporters (By similarity).

    Alternative splice isoforms for CLCN6 Gene

neXtProt entry for CLCN6 Gene

Proteomics data for CLCN6 Gene at MOPED

Post-translational modifications for CLCN6 Gene

Other Protein References for CLCN6 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for CLCN6 Gene

Domains for CLCN6 Gene

Gene Families for CLCN6 Gene

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

Suggested Antigen Peptide Sequences for CLCN6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • P51797
  • Contains 2 CBS domains.
  • Belongs to the chloride channel (TC 2.A.49) family. ClC-6/CLCN6 subfamily.
genes like me logo Genes that share domains with CLCN6: view

Function for CLCN6 Gene

Molecular function for CLCN6 Gene

GENATLAS Biochemistry:
chloride voltage-gated channel 6,97kDa,widely expressed
UniProtKB/Swiss-Prot Function:
Chloride transport protein, initially identified as voltage-gated chloride channel. The presence of the conserved gating glutamate residues suggests that is functions as antiporter

Gene Ontology (GO) - Molecular Function for CLCN6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005216 ion channel activity --
GO:0005247 voltage-gated chloride channel activity NAS 8543009
GO:0005524 ATP binding IEA --
GO:0015297 antiporter activity IEA --
genes like me logo Genes that share ontologies with CLCN6: view

Phenotypes for CLCN6 Gene

genes like me logo Genes that share phenotypes with CLCN6: view

Animal Models for CLCN6 Gene

MGI Knock Outs for CLCN6:

Animal Model Products

miRNA for CLCN6 Gene

miRTarBase miRNAs that target CLCN6

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CLCN6

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for CLCN6 Gene

Localization for CLCN6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLCN6 Gene

Endosome membrane; Multi-pass membrane protein. Note=Detected in detergent-resistant lipid rafts.

Subcellular locations from

Jensen Localization Image for CLCN6 Gene COMPARTMENTS Subcellular localization image for CLCN6 gene
Compartment Confidence
endosome 5
plasma membrane 3

Gene Ontology (GO) - Cellular Components for CLCN6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005765 lysosomal membrane IDA 17897319
GO:0010008 endosome membrane TAS --
GO:0016020 membrane --
GO:0016021 integral component of membrane NAS 8543009
genes like me logo Genes that share ontologies with CLCN6: view

Pathways for CLCN6 Gene

genes like me logo Genes that share pathways with CLCN6: view

Interacting Proteins for CLCN6 Gene

Gene Ontology (GO) - Biological Process for CLCN6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006821 chloride transport NAS 8543009
GO:0006884 cell volume homeostasis NAS 8543009
GO:0007165 signal transduction NAS 8543009
GO:0009612 response to mechanical stimulus IEA --
GO:0034220 ion transmembrane transport TAS --
genes like me logo Genes that share ontologies with CLCN6: view

Compounds for CLCN6 Gene

(1) HMDB Compounds for CLCN6 Gene

Compound Synonyms Cas Number PubMed IDs
  • Cl2

(1) IUPHAR Ligand for CLCN6 Gene

Ligand Type Action Affinity Pubmed IDs
DIDS Channel blocker None

(1) Novoseek inferred chemical compound relationships for CLCN6 Gene

Compound -log(P) Hits PubMed IDs
chloride 65.2 5

(2) PharmGKB related drug/compound annotations for CLCN6 Gene

Drug/compound Annotation
antipsychotics CA
methotrexate CA
genes like me logo Genes that share compounds with CLCN6: view

Transcripts for CLCN6 Gene

Unigene Clusters for CLCN6 Gene

Chloride channel, voltage-sensitive 6:
Representative Sequences:

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for CLCN6

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLCN6 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b · 7c ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^
SP1: - - - - -
SP2: -
SP3: - -
SP4: - -
SP5: - -

ExUns: 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25

Relevant External Links for CLCN6 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLCN6 Gene

mRNA expression in normal human tissues for CLCN6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues for CLCN6 Gene

This gene is overexpressed in Frontal cortex (19.9), Fetal Brain (14.2), Plasma (10.7), Heart (10.3), and Retina (8.1).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for CLCN6 Gene

SOURCE GeneReport for Unigene cluster for CLCN6 Gene Hs.193043

mRNA Expression by UniProt/SwissProt for CLCN6 Gene

Tissue specificity: Testis, ovary, small intestine, brain and skeletal muscle. Low level expression in aortic and coronary vascular smooth muscle cells, and aortic endothelial cells. Isoform 3 is only detected in kidney.
genes like me logo Genes that share expressions with CLCN6: view

Expression partners for CLCN6 Gene

In Situ Assay Products

No data available for mRNA differential expression in normal tissues for CLCN6 Gene

Orthologs for CLCN6 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CLCN6 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia CLCN6 35
  • 91.25 (n)
  • 96.2 (a)
CLCN6 36
  • 96 (a)
(Canis familiaris)
Mammalia CLCN6 35
  • 93.52 (n)
  • 97.7 (a)
CLCN6 36
  • 97 (a)
(Mus musculus)
Mammalia Clcn6 35
  • 90.22 (n)
  • 96.89 (a)
Clcn6 16
Clcn6 36
  • 97 (a)
(Pan troglodytes)
Mammalia CLCN6 35
  • 99.58 (n)
  • 100 (a)
CLCN6 36
  • 100 (a)
(Rattus norvegicus)
Mammalia Clcn6 35
  • 89.8 (n)
  • 96.89 (a)
(Monodelphis domestica)
Mammalia CLCN6 36
  • 96 (a)
(Ornithorhynchus anatinus)
Mammalia CLCN6 36
  • 85 (a)
(Gallus gallus)
Aves CLCN6 35
  • 81.39 (n)
  • 93.43 (a)
CLCN6 36
  • 93 (a)
(Anolis carolinensis)
Reptilia CLCN6 36
  • 87 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia clcn6 35
  • 76.07 (n)
  • 87.92 (a)
(Danio rerio)
Actinopterygii clcn6 35
  • 73.08 (n)
  • 82.97 (a)
wufb95f01 35
clcn6 36
  • 83 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GEF1 36
  • 21 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons CLC-D 35
  • 45.75 (n)
  • 36.96 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 53 (a)
Species with no ortholog for CLCN6:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CLCN6 Gene

Gene Tree for CLCN6 (if available)
Gene Tree for CLCN6 (if available)

Paralogs for CLCN6 Gene

Paralogs for CLCN6 Gene

Selected SIMAP similar genes for CLCN6 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with CLCN6: view

Variants for CLCN6 Gene

Sequence variations from dbSNP and Humsavar for CLCN6 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs169158 -- 11,838,171(+) GGACT(C/T)GGTTT intron-variant
rs171983 -- 11,838,181(+) tgact(A/G)gagag intron-variant
rs198391 -- 11,816,360(+) ATCTG(C/T)AAGGT intron-variant
rs198392 -- 11,819,105(+) CAGCT(A/G)TCATT intron-variant
rs198393 -- 11,819,628(+) TGGGT(C/T)TAACA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CLCN6 Gene

Variant ID Type Subtype PubMed ID
nsv871014 CNV Gain 21882294
nsv871919 CNV Loss 21882294
esv2280942 CNV Deletion 18987734
nsv527521 CNV Loss 19592680

Relevant External Links for CLCN6 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLCN6 Gene

Disorders for CLCN6 Gene

(1) University of Copenhagen DISEASES for CLCN6 Gene

Relevant External Links for CLCN6

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with CLCN6: view

No data available for MalaCards , OMIM , UniProtKB/Swiss-Prot , Novoseek inferred disease relationships and Genatlas for CLCN6 Gene

Publications for CLCN6 Gene

  1. Expression of CLCN voltage-gated chloride channel genes in human blood vessels. (PMID: 10198195) Lamb F.S. … Schutte B.C. (J. Mol. Cell. Cardiol. 1999) 3 4 23
  2. Alternative splicing of ClC-6 (a member of the ClC chloride-channel family) transcripts generates three truncated isoforms one of which, ClC-6c, is kidney-specific. (PMID: 9224655) Eggermont J. … Nilius B. (Biochem. J. 1997) 3 4 23
  3. ClC-6 and ClC-7 are two novel broadly expressed members of the CLC chloride channel family. (PMID: 8543009) Brandt S. … Jentsch T.J. (FEBS Lett. 1995) 2 3 4
  4. Complete genomic structure of the CLCN6 and CLCN7 putative chloride channel genes. (PMID: 10500249) Kornak U. … Kubisch C. (Biochim. Biophys. Acta 1999) 3 4
  5. Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones. (PMID: 12168954) Nakajima D. … Nagase T. (DNA Res. 2002) 3 4

Products for CLCN6 Gene

Sources for CLCN6 Gene

Back to Top