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FLASH GENE
Symbol SCN1A contributors: mct - updated : 03-02-2017
HGNC name sodium channel, voltage-gated, type I, alpha subunit
HGNC id 10585
Corresponding disease
DEL2Q24 chromosome 2 interstitial deletion, including sub-band 2q24.3
GEFSP2 generalized epilepsy with febrile seizures plus, 2
SMEI2 severe myoclonic epilepsy in infancy 2
Location 2q24.3      Physical location : 166.845.670 - 166.930.149
Synonym name
  • sodium channel, brain type 1, alpha subunit
  • sodium channel, voltage-gated, type I, alpha polypeptide
  • Synonym symbol(s) SCN1, NAC1, HBSCI, Nav1.1, SMEI, EIEE6, FEB3, FEB3A, FHM3, GEFSP2
    DNA
    TYPE functioning gene
    SPECIAL FEATURE component of a cluster
    text SCN1A-SCN2A-SCN3A gene cluster
    STRUCTURE 84.48 kb     26 Exon(s)
    10 Kb 5' upstream gene genomic sequence study
    motif repetitive sequence
    MAPPING cloned Y linked N status provisional
    Map cen - SCN9A - SCN1A - D2S2330 - D2S2384 - D2S2363 - D2S2195 - D2S111 - SCN2A2 - D2S124 - SCN3A - D2S382 - D2S2157 - qter
    Authors PMID: 11254445
    RNA
    TRANSCRIPTS type messenger
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    - - 4809 - - - 2007 17436242
  • SCN1A exon 5 splicing
  • NOVA2-mediated modulation of SCN1A exon 5 splicing
  • epilepsy is worse in patients with the AA genotype, therefore requiring higher doses of antiepileptic medication to effectively control the seizures
  • 29 - 8612 229 2009 - 2007 17436242
    28 - 8441 226 1981 - 2007 17436242
    26 - 8100 227.6 1998 - 2007 17436242
    28 - 8426 - 2009 - 2007 17436242
    27 - 8433 - 2009 - 2007 17436242
    27 - 8301 - 1998 - 2007 17436242
    28 - 8393 - 1998 - 2007 17436242
    27 - 8400 - 1998 - 2007 17436242
    28 - 8492 - 1998 - 2007 17436242
    28 - 8449 - 1997 - 2007 17436242
    27 - 8397 - 1997 - 2007 17436242
    27 - 8349 - 1981 - 2007 17436242
    28 - 8342 - 1982 - 2007 17436242
    27 - 8438 - 1980 - 2007 17436242
    28 - 8508 - 1195 - 2007 17436242
    EXPRESSION
    Type restricted
       expressed in (based on citations)
    organ(s)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    Nervousbrainlimbic systemhippocampus   Mus musculus
    Visualeye    
    tissue
    SystemTissueTissue level 1Tissue level 2LevelPubmedSpeciesStageRna symbol
    Muscularstriatumskeletal  
    cells
    SystemCellPubmedSpeciesStageRna symbol
    Nervousneuron Mus musculus
    cell lineage
    cell lines
    fluid/secretion
    at STAGE
    PROTEIN
    PHYSICAL PROPERTIES Hydrophobic
    STRUCTURE
    motifs/domains
  • four domains of homology, each with six alpha helical membrane spanning segments
  • two cytoplasmic loops
  • mono polymer monomer
    HOMOLOGY
    interspecies homolog to murine Scn1a
    intraspecies homolog to SCN8A
    Homologene
    FAMILY
  • sodium channel family
  • CATEGORY transport channel
    SUBCELLULAR LOCALIZATION     plasma membrane
        intracellular
    intracellular,nucleus,nucleoplasm,nuclear bodies
    basic FUNCTION
  • mediating the voltage-dependent sodium ion permeability of excitable membranes
  • having a slope conductance (17 pS) similar to channels found in native mammalian neurons
  • is the primary voltage-gated Na(+) channel in several classes of GABAergic interneurons, and its reduced activity leads to reduced excitability and decreased GABAergic tone
  • in axon initial segments of bipolar cells augment input to magnocellular visual pathways in the primate retina
  • plays a critical role in the initiation of action potential in the central nervous system
  • CELLULAR PROCESS
    PHYSIOLOGICAL PROCESS electron transport
    PATHWAY
    metabolism
    signaling
    a component
  • protein constituent of membrane
  • INTERACTION
    DNA
    RNA
    small molecule
    protein
  • interacting with NOVA2 (specific regulatory role of NOVA2 in controlling a clinically significant alternative splicing of SCN1A)
  • potential involvement of RACK1 in negatively regulating SCN1A transcription via interaction with the silencer
  • RER1 controls the assembly and transport of SCN1A, SCN8A, the principal sodium channels responsible for recurrent firing, in Purkinje cell (PC)
  • cell & other
    REGULATION
    ASSOCIATED DISORDERS
    corresponding disease(s) GEFSP2 , SMEI2 , DEL2Q24
    Other morbid association(s)
    TypeGene ModificationChromosome rearrangementProtein expressionProtein Function
    constitutional germinal mutation      
    sporadic autistic disorder
    constitutional       loss of function
    may disrupt information processing in Dravet syndrom via a dysregulation of brain rhythms
    constitutional       loss of function
    dysfunction in SCN1A is increasingly being linked to neuropsychiatric abnormalities, social deficits and cognitive disabilities
    Susceptibility
  • to Rasmussen encephalitis
  • to Dravet syndrome
  • to autism spectrum disorder
  • Variant & Polymorphism other
  • R1575C mutation identified in a patient with Rasmussen encephalitis
  • putative disease-associated haplotype in two patients affected with Dravet syndrome
  • Candidate gene
    Marker
    Therapy target
    ANIMAL & CELL MODELS
  • mice with Scn1a haploinsufficiency display hyperactivity, stereotyped behaviors, social interaction deficits, and impaired context-dependent spatial memory
  • Scn1a+/- mice exhibit hyperactivity, increased anxiety, and increased stereotyped behaviors, which are phenocopies of autistic traits in Dravet sdr