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FLASH GENE
Symbol SCN5A contributors: mct - updated : 04-09-2013
HGNC name sodium channel, voltage-gated, type V, alpha subunit
HGNC id 10593
Corresponding disease
BRGS1 Brugada syndrome 1
CMD1E cardiomyopathy, dilated 1E
LQT3 long QT syndrome with ventricular tachyarrhythmia, type 3
PCCD1 progressive cardiac conduction defect 1
PCCD2 progressive cardiac conduction defect 2
SSS1 Sick sinus syndrome 1
Location 3p22.2      Physical location : 38.589.553 - 38.691.164
Synonym name
  • cardiac sodium channel alpha subunit
  • sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)
  • Synonym symbol(s) IVF, HB2, HB1, Nav1.5, CDCD2, CMPD2, HB1, HB2, HBBD, HH1, ICCD, VF1
    DNA
    TYPE functioning gene
    STRUCTURE 101.61 kb     28 Exon(s)
    10 Kb 5' upstream gene genomic sequence study
    regulatory sequence Promoter
    cytosine-phosphate-guanine/HTF
    motif repetitive sequence
    text structure
  • dinucleotide repeat polymorphism in intron 16
  • multiple positive and negative cis-acting elements extending into intron 1
  • MAPPING cloned Y linked N status confirmed
    Physical map
    CTDSPL 3p21.3 CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like VILL 3p21.3 CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase-like PLCD1 3p21.3 phospholipase C, delta 1 DLEC1 ACAA1 3p23-p22 acetyl-Coenzyme A acyltransferase 1 (peroxisomal 3-oxoacyl-Coenzyme A thiolase) MYD88 3p22-p21.3 myeloid differentiation primary response gene (88) OSR1 3p22-p21.3 oxidative-stress responsive 1 SLC22A13 3p22-p21.3 solute carrier family 22 (organic cation transporter), member 13 SLC22A14 3p22-p21.3 solute carrier family 22 (organic cation transporter), member 14 XYLB 3p22-p21.3 xylulokinase homolog (H. influenzae) ACVR2B 3p22 activin A receptor, type IIB ENDOGL1 3p21.3 endonuclease G-like 1 LOC391528 3 similar to ribosomal protein L18a; 60S ribosomal protein L18a SCN5A 3p21 sodium channel, voltage-gated, type V, alpha (long QT syndrome 3) SCN10A 3p21-p22 sodium channel, voltage-gated, type X, alpha SCN11A 3p24-p21 sodium channel, voltage-gated, type XI, alpha KIAA1449 3p21.33 WD repeat endosomal protein GORASP1 3p22-p21.33 golgi reassembly stacking protein 1, 65kDa STI2 3p21.33 TPR domain containing STI2 AXUD1 3p22 AXIN1 up-regulated 1 CMYA1 3p21.33 cardiomyopathy associated 1 CX3CR1 3p21.32-p21.31 chemokine (C-X3-C motif) receptor 1 CCR8 3p21.32-p21.31 chemokine (C-C motif) receptor 8 hnRNPA1p 3p21.33 heterogeneous nuclear ribonucleoprotein A1 pseudogene
    RNA
    TRANSCRIPTS type messenger
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    28 - 8504 227 2016 - 2008 18378609
    28 - 8501 227 2015 - 2008 18378609
    27 - 8450 225 1998 - 2008 18378609
    28 - 8504 227 2016 - 2008 18378609
    27 - 8343 221.2 1962 - -
    also called isoform f
    28 - 8406 223 1983 - -
    also called isoform e
    EXPRESSION
    Type restricted
       expressed in (based on citations)
    organ(s)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    Cardiovascularheartatrium   
    Reproductivefemale systemovary   
    tissue
    SystemTissueTissue level 1Tissue level 2LevelPubmedSpeciesStageRna symbol
    Muscularstriatumcardiacmyocardium  Homo sapiens
    cells
    SystemCellPubmedSpeciesStageRna symbol
    Muscularmyocyte Homo sapiens
    cell lineage
    cell lines
    fluid/secretion
    at STAGE
    PROTEIN
    PHYSICAL PROPERTIES
    STRUCTURE
    motifs/domains
  • four transmembrane domains (4TM) of homology, each with six alpha helical membrane spanning segments
  • two cytoplasmic loops
  • dinucleotide repeat polymorphism
  • one IQ domain
  • C-terminus with a PY-motif (xPPxY) acting as binding site for Nedd4/Nedd4-like ubiquitin-protein ligases
  • HOMOLOGY
    interspecies homolog to murine Scn5a
    Homologene
    FAMILY
    CATEGORY transport channel
    SUBCELLULAR LOCALIZATION     plasma membrane
        intracellular
    intracellular,cytoplasm,organelle,membrane
    intracellular,cytoplasm,organelle,endoplasmic reticulum
    text
  • SCN5A and DLG1 are both localized at intercalated discs
  • localizes at lateral membranes of cardiomyocytes with dystrophin and syntrophin
  • basic FUNCTION
  • sodium voltage-gated channel, type V, tetradotoxin-resistant, playing a critical role for heart excitability and conduction
  • CELLULAR PROCESS
    PHYSIOLOGICAL PROCESS
    PATHWAY
    metabolism
    signaling
    a component
  • SNTA1-based NOS1 complex attached to SCN5A is a key regulator of sodium current
  • INTERACTION
    DNA
    RNA
    small molecule
    protein
  • interacting with NEDD4L (acting on SCN5A by decreasing the channel density at the cell surface)
  • interacting with TCAP
  • TBX5 drives SCN5A expression to regulate cardiac conduction system function
  • GJA1 associates with SCN5A in the cardiomyocyte perinexus
  • cell & other
    REGULATION
    ASSOCIATED DISORDERS
    corresponding disease(s) LQT3 , PCCD2 , PCCD1 , SSS1 , CMD1E , BRGS1
    related resource Congenital Long QT Syndrome at GeneDis
    Gene Connection for the Heart
    Long QT Syndrome Database
    Susceptibility to cardiac arrhythmia and sudden death
    Variant & Polymorphism SNP , other
  • Y1102 and H558R allele increasing risk of arrhythmia
  • SNP S1103Y associated with cardiac arrhythmia and sudden death
  • rs11720524 located in intron 1 in SCN5A remained significantly associated with sudden/arrhythmic death
  • Candidate gene
    Marker
    Therapy target
    ANIMAL & CELL MODELS