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Gene

SCN1A

sodium voltage-gated channel alpha subunit 1

Summary

Cytogenetic location
2q24.3
Coordinates
Chromosome 2: 165,985,813–166,128,020 (GRCh38)
Exons
29 exons across 142.2 kb
Protein
2,009 amino acids
Inheritance
Autosomal dominant
Also known as
Nav1.1, GEFSP2, HBSCI, NAC1, SMEI
Previous symbols
SCN1, FEB3
MANE Select transcript
ENST00000674923.1NM_001165963.4
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • Dravet Syndrome

    • Autosomal dominant

      Dravet syndrome is a channelopathy with epilepsy of with onset during the first year of life, typically 4-5 months, characterized by status epilepticus and a variety of drug-resistant seizures often induced by fever, presenting in previously healthy children, and which frequently leads to cognitive and motor impairment. Dravet differs from other channelopathies usually due to a mutation in SCN1A.

      • ClinGen rates the link definitive
      • 2 GenCC submitters rate it definitive or strong
      What knowing changes

      Valproate, clobazam, topiramate, stiripentol; fenfluramine (Fintepla) and cannabidiol (Epidiolex) for drug-resistant cases; sodium channel blockers (lamotrigine, carbamazepine, oxcarbazepine) are CONTRAINDICATED in SCN1A-positive patients

  • Familial Hemiplegic Migraine

    • Migraine, Familial Hemiplegic, 3Autosomal dominant

      Any familial or sporadic hemiplegic migraine in which the cause of the disease is a mutation in the SCN1A gene.

      • 2 GenCC submitters rate it definitive or strong
    • Autosomal dominant

      A migraine disorder characterized by individual and family history of aura that includes motor weakness.

      • 2 GenCC submitters rate it definitive or strong
    • Familial Or Sporadic Hemiplegic MigraineAutosomal dominant

      Hemiplegic migraine (HM) is a rare variety of migraine with aura characterized by the presence of a motor weakness during the aura. Hemiplegic migraine has two main forms depending on the familial history: patients with at least one first- or second-degree relative who has aura including motor weakness have familial hemiplegic migraine (FHM); patients without such familial history have sporadic hemiplegic migraine (SHM).

      • 2 GenCC submitters rate it definitive or strong

Broader groupings

  • Epilepsy (Full Panel)

    • Epilepsy

      One of 171 genes linked to it

      A brain disorder characterized by episodes of abnormally increased neuronal discharge resulting in transient episodes of sensory or motor neurological dysfunction, or psychic dysfunction. These episodes may or may not be associated with loss of consciousness or convulsions.

      • ClinGen rates the link definitive
      • 6 GenCC submitters rate it definitive or strong

Inheritance

Autosomal dominant
One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.

How SCN1A is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
  • Variants with a page
Chromosome 2, with a bracket where SCN1A sits. SCN1A and 5 genes near it on chromosome 2, from 165,556,917 to 166,556,916.Chromosome 22q24.3p25.3p25.2p25.1p24.3p24.2p24.1p23.3p23.2p23.1p22.3p22.2p22.1p21p16.3p16.2p16.1p15p14p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13q14.1q14.2q14.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q34q35q36.1q36.2q36.3q37.1q37.2q37.3165.6 Mb165.8 Mb166 Mb166.2 Mb166.4 MbCSRNP3: 165,469,647–165,689,407, forward strandCSRNP3GALNT3: 165,747,339–165,846,201, reverse strandGALNT3TTC21B: 165,857,475–165,953,851, reverse strandTTC21BSCN1A: 165,985,813–166,128,020, reverse strandSCN1ASCN9A: 166,195,185–166,376,001, reverse strandSCN9ASCN7A: 166,403,472–166,611,482, reverse strandSCN7ADiagram of SCN1A: 29 exons on the reverse strand of chromosome 2Exon 29: 124 known disease-causing sitesExon 28: 21 known disease-causing sitesExon 27: 13 known disease-causing sitesExon 26: 18 known disease-causing sitesExon 25: 7 known disease-causing sitesExon 24: 46 known disease-causing sitesExon 23: 17 known disease-causing sitesExon 22: 26 known disease-causing sitesExon 21: 16 known disease-causing sitesExon 20: 10 known disease-causing sitesExon 19: 25 known disease-causing sitesExon 18: 55 known disease-causing sitesExon 17: 16 known disease-causing sitesExon 16: 18 known disease-causing sitesExon 15: 8 known disease-causing sitesExon 14: 22 known disease-causing sitesExon 13: 14 known disease-causing sitesExon 12: 32 known disease-causing sitesExon 11: 30 known disease-causing sitesExon 10: 11 known disease-causing sitesExon 9: 39 known disease-causing sitesExon 8: 17 known disease-causing sitesExon 7: 13 known disease-causing sitesExon 6: 7 known disease-causing sitesExon 5: 20 known disease-causing sitesExon 4: 20 known disease-causing sitesExon 29: 165,985,813–165,992,422, 6,610 bases. 4 variants with a page in exon 29. List themExon 28: 165,994,146–165,994,416, 271 basesExon 27: 165,996,013–165,996,117, 105 basesExon 26: 165,998,038–165,998,175, 138 basesExon 25: 165,999,723–165,999,776, 54 basesExon 24: 166,002,472–166,002,753, 282 basesExon 23: 166,009,719–166,009,841, 123 basesExon 22: 166,012,109–166,012,282, 174 basesExon 21: 166,013,744–166,013,898, 155 bases. 1 variant with a page in exon 21. List themExon 20: 166,015,607–166,015,727, 121 basesExon 19: 166,036,048–166,036,530, 483 basesExon 18: 166,037,776–166,038,132, 357 bases. 2 variants with a page in exon 18. List themExon 17: 166,039,423–166,039,596, 174 basesExon 16: 166,041,231–166,041,469, 239 bases. 1 variant with a page in exon 16. List themExon 15: 166,042,292–166,042,424, 133 basesExon 14: 166,043,669–166,044,049, 381 bases. 1 variant with a page in exon 14. List themExon 13: 166,045,043–166,045,327, 285 basesExon 12: 166,046,770–166,046,976, 207 bases. 1 variant with a page in exon 12. List themExon 11: 166,047,627–166,047,768, 142 basesExon 10: 166,048,886–166,048,949, 64 basesExon 9: 166,051,719–166,051,988, 270 basesExon 8: 166,052,852–166,052,943, 92 bases. 2 variants with a page in exon 8. List themExon 7: 166,054,638–166,054,766, 129 basesExon 6: 166,056,411–166,056,500, 90 basesExon 5: 166,058,570–166,058,688, 119 basesExon 4: 166,073,358–166,073,670, 313 basesExon 3: 166,077,710–166,077,801, 92 basesExon 2: 166,126,924–166,127,010, 87 basesExon 1: 166,127,771–166,128,020, 250 bases2925201510515′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 11.9 kb of the gene's 142.2 kb; 6,030 of those bases code for the protein.

How a genome test reads SCN1A

720

positions in SCN1A where ClinVar classes a change as pathogenic or likely pathogenic

49 of them (6.8%) fall in regions short reads find hard.

  • Low mappability (49 sites)Regions where 100 bp or 250 bp reads cannot be placed uniquely.

A whole genome covers all 142.2 kb of SCN1A, introns included, not only the 11.9 kb of exons.

Variants with a page (12)

The SCN1A variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.

VariantHGVS c.Exon or intronPosition (GRCh38)ClinVar classificationReview status
A420Vc.1259C>TExon 12166,046,888Likely pathogenic3 stars out of 4 reviewed by expert panel
G908Rc.2722G>CExon 18166,038,000Likely pathogenic3 stars out of 4 reviewed by expert panel
P768Lc.2303C>TExon 16166,041,343Likely pathogenic3 stars out of 4 reviewed by expert panel
P1838Lfs*20c.5511delExon 29165,991,763Likely pathogenic3 stars out of 4 reviewed by expert panel
R219Gc.655A>GExon 8166,052,891Likely pathogenic3 stars out of 4 reviewed by expert panel
R219Tc.656G>CExon 8166,052,890Likely pathogenic3 stars out of 4 reviewed by expert panel
R931Hc.2792G>AExon 18166,037,930Pathogenic3 stars out of 4 reviewed by expert panel
R1639Pc.4916G>CExon 29165,992,359Pathogenic3 stars out of 4 reviewed by expert panel
S570Nc.1709G>AExon 14166,044,003Likely pathogenic3 stars out of 4 reviewed by expert panel
T1210Mc.3629C>TExon 21166,013,820Likely pathogenic3 stars out of 4 reviewed by expert panel

See all 12 SCN1A variants →

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). SCN1A gene: sodium voltage-gated channel alpha subunit 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/scn1a

Vancouver

Dante Labs. SCN1A gene: sodium voltage-gated channel alpha subunit 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/scn1a

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