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FLASH GENE
Symbol CLCN6 contributors: mct - updated : 09-12-2020
HGNC name chloride channel 6
HGNC id 2024
DNA
TYPE functioning gene
STRUCTURE 36.94 kb     23 Exon(s)
Genomic sequence alignment details
10 Kb 5' upstream gene genomic sequence study
regulatory sequence cytosine-phosphate-guanine/HTF
motif repetitive sequence   triplet
text structure
  • CA repeat in intron 2
  • DNA methylation levels at several individual age-associated CpGs seem to be associated with life expectancy - e.g., at CpGs associated with the genes PDE4C and CLCN6
    • MAPPING cloned Y linked N status confirmed
    RNA
    TRANSCRIPTS type messenger
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    23 polyA site 5589 97.2 869 - 1997 9224655
  • CLC-6a
    • - polyA site 3894 36 320 widely 1997 9224655
    truncated at C terminus, four TM segment
    - polyA site 3993 38.8 353 kidney specific 1997 9224655
    truncated at C terminus, six TM segment
    - polyA site 3858 34.5 308 widely 1997 9224655
    truncated at C terminus, four TM segment
    22 - 5523 - 847 - 1997 9224655
    EXPRESSION
    Type widely
       expressed in (based on citations)
    organ(s)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    Cardiovascularvesselsaorta   
    Digestivemouth   highly
    Endocrineparathyroid   highly
    Nervousnerve   highly
    Reproductivefemale systemovary   
     male systemtestis   
    tissue
    SystemTissueTissue level 1Tissue level 2LevelPubmedSpeciesStageRna symbol
    Epithelialbarrier/lining   
    Muscularsmooth   
    Muscularstriatumskeletal  
    Nervouscentral  predominantly Homo sapiens
    cells
    SystemCellPubmedSpeciesStageRna symbol
    Cardiovascularendothelial cell
    Nervousneuron
    cell lineage
    cell lines
    fluid/secretion
    at STAGE
    PROTEIN
    PHYSICAL PROPERTIES
    STRUCTURE
    motifs/domains
  • twelve alpha helical membrane spanning protein cytoplasmic N and C terminals
  • two CBS forming a stable globular domain
    • HOMOLOGY
    interspecies homolog to murine Clcn6
    Homologene
    FAMILY CLCN family
    CATEGORY transport channel
    SUBCELLULAR LOCALIZATION     plasma membrane
        intracellular
    intracellular,cytoplasm,organelle,membrane
    intracellular,cytoplasm,organelle,endosome
    intracellular,cytoplasm,organelle,lysosome
    text
  • colocalized with markers for late endosomes in neuronal cell bodies
  • predominantly found in late endosomes of the nervous system
    • basic FUNCTION
  • chloride voltage-gated channel, regulating cell volume, membrane potential stabilization, transepithelial transport
  • CLCN6 is a Cl(-)/H(+) antiporter
    • CELLULAR PROCESS
    PHYSIOLOGICAL PROCESS cellular trafficking transport
    PATHWAY
    metabolism
    signaling
    a component
    INTERACTION
    DNA
    RNA
    small molecule
    protein
    cell & other
    REGULATION
    ASSOCIATED DISORDERS
    corresponding disease(s) DDHRND
    Susceptibility to epilepsy disorders
    Variant & Polymorphism other
  • pathogenic and likely pathogenic variants in CLCN6 in epilepsy disorders
    • Candidate gene
    Marker
    Therapy target
    ANIMAL & CELL MODELS
  • Clcn6 -/- mice have only mild neuronal lysosomal storage abnormalities