Sodium Voltage-Gated Channel, Alpha Subunit 1

Alternative Names

  • SCN1A
  • Sodium Channel, Neuronal Type I, Alpha Subunit
  • Sodium Channel, Brain Type I, Alpha Subunit
  • NAC1
  • NAV1.1
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OMIM Number

182389

NCBI Gene ID

6323

Uniprot ID

P35498

Length

164,632 bases

No. of Exons

31

No. of isoforms

3

Protein Name

Sodium channel protein type 1 subunit alpha

Molecular Mass

228972 Da

Amino Acid Count

2009

Genomic Location

chr2:165,984,641-166,149,272

Gene Map Locus
2q24.3

Description

The SCN1A gene encodes the large alpha subunit of the voltage-gated sodium channels (NaV) called NaV1.1. Voltage-sensitive sodium channels are heteromeric complexes consisting of a large central pore-forming glycosylated alpha subunit and 2 smaller auxiliary beta subunits. These channels are responsible for action potential initiation and propagation in excitable cells, including nerve, muscle, and neuroendocrine cell types. They are also expressed at low levels in non-excitable cells, where their physiological role is unclear.

Mutations in the SCN1A gene cause a spectrum of seizure disorders, ranging from early-onset isolated febrile seizures to generalized epilepsy with febrile seizures plus, type 2, which represents a more severe phenotype. Other conditions cause more serious seizures that last longer and may be difficult to control. These recurrent seizures can worsen over time and lead to a decline in brain function. Severe seizure disorders caused by SCN1A mutations include severe myoclonic epilepsy of infancy (SMEI), also called Dravet syndrome, and intractable childhood epilepsy with generalized tonic-clonic seizures (ICE-GTC). In addition to epileptic disorders, at least three mutations in the SCN1A gene have been identified in people with familial hemiplegic migraine type 3 (FHM3).

Epidemiology in the Arab World

View Map
Variant NameCountryGenomic LocationClinvar Clinical SignificanceCTGA Clinical Significance Condition(s)HGVS ExpressionsdbSNPClinvar
NM_001165963.3:c.2593C>TLebanonchr2:166038129PathogenicPathogenicDravet SyndromeNG_011906.1:g.40511C>T; NM_001165963.3:c.2593C>T; NP_001340877.1:p.Arg865Ter794726697189844
NM_001165963.3:c.4907G>ALebanonchr2:165992368Likely Pathogenic, PathogenicPathogenicDravet SyndromeNG_011906.1:g.86272G>A; NM_001165963.3:c.4907G>A; NP_001340877.1:p.Arg1636Gln12191799568557
NM_001165963.4:c.2824C>GSaudi ArabiaNC_000002.12:g.166037898G>CLikely PathogenicDravet SyndromeNG_011906.1:g.40742C>G; NM_001165963.4:c.2824C>G; NP_001340877.1:p.Leu942Val
NM_001165963.4:c.2836C>TLebanonchr2:166037886PathogenicPathogenicDravet SyndromeNG_011906.1:g.40754C>T; NM_001165963.4:c.2836C>T; NP_001340877.1:p.Arg946Cys12191877568604
NM_001165963.4:c.3607C>TSaudi ArabiaNC_000002.12:g.166013842G>APathogenicLikely PathogenicDravet SyndromeNG_011906.1:g.64798C>T; NM_001165963.4:c.3607C>T; NP_001340886.1:p.Gln1175Ter796052995206803
NM_001165963.4:c.428T>CLebanonchr2:166056456PathogenicDravet SyndromeNG_011906.1:g.22184T>C; NM_001165963.4:c.428T>C; NP_001340877.1:p.Val143Ala
NM_001165963.4:c.4313T>CLebanonNC_000002.12:g.165999748A>GPathogenicLikely PathogenicDravet SyndromeNG_011906.1:g.78892T>C; NM_001165963.4:c.4313T>C; NP_001159435.1:p.Met1438Thr7960530101393964
NM_001165963.4:c.4497delSaudi ArabiaNC_000002.12:g.165996097delLikely PathogenicDravet SyndromeNG_011906.1:g.82543del; NM_001165963.4:c.4497del; NP_001340877.1:p.Phe1499LeufsTer2
NM_001165963.4:c.4513A>TLebanonchr2:165996081PathogenicDravet SyndromeNG_011906.1:g.82559A>T; NM_001165963.4:c.4513A>T; NP_001340877.1:p.Lys1505Ter1553521524
NM_001165963.4:c.5195C>TLebanonNC_000002.12:g.165992080G>APathogenicLikely PathogenicDravet SyndromeNG_011906.1:g.86560C>T; NM_001165963.4:c.5195C>T; NP_001159435.1:p.Pro1732Leu1455797
NM_001165963.4:c.5536_5539delUnited Arab EmiratesNC_000002.12:g.165991737TTTG[1]PathogenicPathogenicDravet SyndromeNG_011906.1:g.86897AAAC[1]; NM_001165963.4:c.5536_5539del; NP_001159435.1:p.Lys1846SerfsTer11794726726189881
NM_001165963.4:c.602+2dupTLebanonchr2:166054636PathogenicPathogenicDravet SyndromeNG_011906.1:g.24004dup; NM_001165963.4:c.602+2dupT796053054206892
NM_001165963.4:c.677C>TSaudi ArabiaNC_000002.12:g.166052869G>APathogenicLikely PathogenicDravet SyndromeNG_011906.1:g.25771C>T; NM_001165963.4:c.677C>T; NP_001159435.1:p.Thr226Met12191798468578
NM_001165963.4:c.715G>CSaudi ArabiaNC_000002.12:g.166051968C>GLikely PathogenicDravet SyndromeNG_011906.1:g.26672G>C; NM_001165963.4:c.715G>C; NP_001159435.1:p.Ala239Pro

Other Reports

Tunisia

Mrabet et al. (2007) studied the possible association of mutations of the SCN1A, SCN1B and GABRG2 genes with generalized epilepsy with febrile seizure plus (GEFS+) in two unrelated multigenerational Tunisian families affected with GEFS+ spectrum. Screening of the known SCN1B, SCN1A and GABRG2 gene mutations by direct sequencing excluded the involvement of all known published mutations. However, a novel single insertion of a T nucleotide at a heterozygous state within the intron 12 of the SCN1A gene (IVS12-11insT) was identified in two probands and their parents with a possible pathogenic role in the expression of the GEFS+ disease. Mrabet et al. (2007) hypothesized that this mutation may affect the regulatory elements contained in the intron, influence the splicing system or affect the transcription state, and, subsequently, modify the alpha subunit protein. Another hypothesis is that this insertion may be considered as a specific polymorphism for the Tunisian population. The IVS12-11insT variant is situated in the non-coding part and was present in both affected and unaffected individuals. Nevertheless, no data have been published in the literature about this variant in the Tunisian population, suggesting then that this genetic finding could play a role in predisposing subjects to seizures. Mrabet et al. (2007) concluded that the results obtained from this study corroborate the genetic heterogeneity of GEFS+ predominantly in epilepsy patients of different countries and ethnic groups.

Fendri-Kriaa et al. (2009) conducted a gene-association study to depict the molecular basis of GEFS+ in two affected Tunisian families. Statistical analysis pointed to GABRG2 on the GEFS+3 locus and SCN1A on the GEFS+2 locus as potential candidate genes. Sequencing analysis of the SCN1A gene showed a known mutation (c.1811G>A) and a putative disease-associated haplotype in only one family.

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