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Aliases for CLCN6 Gene

Aliases for CLCN6 Gene

  • Chloride Voltage-Gated Channel 6 2 3 5
  • 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 Voltage-Gated Channel 6) is a Protein Coding gene. Diseases associated with CLCN6 include Benign Familial Infantile Epilepsy. Among its related pathways are Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds and HIV Life Cycle. GO annotations related to this gene include ion channel activity and voltage-gated chloride channel 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 CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLCN6 Gene

Genomics for CLCN6 Gene

Regulatory Elements for CLCN6 Gene

Enhancers for CLCN6 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01G011795 1.6 Ensembl ENCODE dbSUPER 18.2 -8.7 -8700 4.6 HDGF PKNOX1 CREB3L1 MLX ARNT ZFP64 ARID4B SIN3A SLC30A9 ZNF766 CLCN6 NPPA-AS1 MTHFR AGTRAP NPPB ENSG00000271895 FBXO44 GC01M011785
GH01G011800 1.4 ENCODE dbSUPER 19.4 -1.9 -1868 8.3 MLX CREB3L1 AGO1 DMAP1 YY1 ZNF263 SP3 NFYC MEF2D ZNF610 CLCN6 EXOSC10 MTHFR NPPA-AS1 ENSG00000271895 UBIAD1 ENSG00000226849 TNFRSF8 MIIP GC01M011785
GH01G011784 1.6 Ensembl ENCODE dbSUPER 15.1 -17.4 -17444 9.2 HDGF PKNOX1 ARNT CREB3L1 AGO1 ZFP64 SIN3A ARID4B ZNF2 YY1 MTHFR NPPA-AS1 CLCN6 AGTRAP NPPB PIR55960 GC01M011790 LOC102724659
GH01G011813 1.2 Ensembl ENCODE dbSUPER 19.1 +8.8 8773 2.4 CTCF ZNF263 RFX1 MTA2 NR2F1 CEBPB DPF2 TBX21 RARA IKZF1 NPPA-AS1 CLCN6 NPPB PLOD1 KIAA2013 MTHFR
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CLCN6 on UCSC Golden Path with GeneCards custom track

Promoters for CLCN6 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000250241 -196 2201 MLX CREB3L1 AGO1 DMAP1 YY1 SP3 NFYC ZNF610 GLIS1 NBN

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

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

Genes around CLCN6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLCN6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

Post-translational modifications for CLCN6 Gene

  • N-glycosylated on several asparagine residues.
  • Ubiquitination at Lys224
  • Glycosylation at posLast=410410, posLast=422422, and Asn432
  • Modification sites at PhosphoSitePlus

Other Protein References for CLCN6 Gene

No data available for DME Specific Peptides for CLCN6 Gene

Domains & Families for CLCN6 Gene

Gene Families for CLCN6 Gene

Suggested Antigen Peptide Sequences for CLCN6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the chloride channel (TC 2.A.49) family. ClC-6/CLCN6 subfamily.
  • 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 IEA --
GO:0005247 voltage-gated chloride channel activity NAS 8543009
GO:0005524 ATP binding IEA --
GO:0015297 antiporter activity TAS --
genes like me logo Genes that share ontologies with CLCN6: view
genes like me logo Genes that share phenotypes with CLCN6: view

Animal Models for CLCN6 Gene

MGI Knock Outs for CLCN6:

Animal Model Products

  • Taconic Biosciences Mouse Models for CLCN6

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets 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

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLCN6 gene
Compartment Confidence
lysosome 5
endosome 5
plasma membrane 4
cytosol 2

Gene Ontology (GO) - Cellular Components for CLCN6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005765 lysosomal membrane IDA 17897319
GO:0005768 endosome IEA --
GO:0010008 endosome membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane NAS 8543009
genes like me logo Genes that share ontologies with CLCN6: view

Pathways & Interactions for CLCN6 Gene

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

Gene Ontology (GO) - Biological Process for CLCN6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006811 ion transport IEA --
GO:0006821 chloride transport NAS 8543009
GO:0006884 cell volume homeostasis NAS 8543009
GO:0007165 signal transduction NAS 8543009
genes like me logo Genes that share ontologies with CLCN6: view

No data available for SIGNOR curated interactions for CLCN6 Gene

Drugs & Compounds for CLCN6 Gene

(5) Drugs for CLCN6 Gene - From: PharmGKB, DGIdb, and IUPHAR

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Fluorouracil Approved Pharma RNA processing inhibitor and thymidylate synthase inhibitor 1856
Oxaliplatin Approved, Investigational Pharma Antitumor agent, Platinum 1460
leucovorin Approved Nutra 3235,1128
DIDS Pharma Channel blocker 0
antipsychotics Pharma 0

(2) Additional Compounds for CLCN6 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Chloride ion
  • Bertholite
  • Chloor
  • Chlor
  • Chlore
  • Chloride
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:

CRISPR Products

Inhibitory RNA 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 from GTEx, Illumina, BioGPS, and CGAP SAGE for CLCN6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED 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 in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CLCN6 Gene

Protein tissue co-expression partners for CLCN6 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CLCN6 Gene:


SOURCE GeneReport for Unigene cluster for CLCN6 Gene:


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.

Evidence on tissue expression from TISSUES for CLCN6 Gene

  • Nervous system(4.8)
  • Bone marrow(4.2)
  • Muscle(4.2)
genes like me logo Genes that share expression patterns with CLCN6: view

Primer Products

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
(Pan troglodytes)
Mammalia CLCN6 34 35
  • 99.58 (n)
(Monodelphis domestica)
Mammalia CLCN6 35
  • 96 (a)
(Canis familiaris)
Mammalia CLCN6 34 35
  • 93.52 (n)
(Bos Taurus)
Mammalia CLCN6 34 35
  • 91.25 (n)
(Mus musculus)
Mammalia Clcn6 34 16 35
  • 90.22 (n)
(Rattus norvegicus)
Mammalia Clcn6 34
  • 89.8 (n)
(Ornithorhynchus anatinus)
Mammalia CLCN6 35
  • 85 (a)
(Gallus gallus)
Aves CLCN6 34 35
  • 81.39 (n)
(Anolis carolinensis)
Reptilia CLCN6 35
  • 87 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia clcn6 34
  • 76.07 (n)
(Danio rerio)
Actinopterygii clcn6 34 35
  • 73.08 (n)
wufb95f01 34
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GEF1 35
  • 21 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons CLC-D 34
  • 45.75 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 53 (a)
Species where no ortholog for CLCN6 was found in the sources mined by GeneCards:
  • 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

(1) 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
rs886045193 Uncertain significance 11,805,889(-) CTGGA(A/G)GGTGA upstream-variant-2KB, utr-variant-5-prime
rs886045194 Uncertain significance 11,805,937(-) CTGCA(-/GCGGCCA)CAGTG upstream-variant-2KB, utr-variant-5-prime
rs1000000481 -- 11,813,337(+) AGTCT(A/G)GTTTC intron-variant
rs1000021406 -- 11,833,116(+) ATTTT(C/T)CTCCC intron-variant
rs1000097776 -- 11,825,112(+) ACCTC(A/G)AAGCT intron-variant

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

Variant ID Type Subtype PubMed ID
esv2280942 CNV deletion 18987734
nsv527521 CNV loss 19592680

Variation tolerance for CLCN6 Gene

Residual Variation Intolerance Score: 2.78% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.07; 60.81% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CLCN6 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

Disorders for CLCN6 Gene

MalaCards: The human disease database

(1) MalaCards diseases for CLCN6 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
benign familial infantile epilepsy
  • benign familial infantile convulsion
- elite association - COSMIC cancer census association via MalaCards
Search CLCN6 in MalaCards View complete list of genes associated with diseases

Relevant External Links for CLCN6

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with CLCN6: view

No data available for UniProtKB/Swiss-Prot 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 22 64
  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 22 64
  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 64
  4. 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. (PMID: 21273288) Del Greco M F. … Pramstaller P.P. (Hum. Mol. Genet. 2011) 3 46 64
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64

Products for CLCN6 Gene

Sources for CLCN6 Gene

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