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Gene

SCN2A

sodium voltage-gated channel alpha subunit 2

Summary

Cytogenetic location
2q24.3
Coordinates
Chromosome 2: 165,239,414–165,392,304 (GRCh38)
Exons
27 exons across 152.9 kb
Protein
2,005 amino acids
Inheritance
Autosomal dominant
Also known as
Nav1.2, HBSCII, HBSCI
Previous symbols
SCN2A1, SCN2A2
MANE Select transcript
ENST00000375437.7NM_001040142.2
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

  • Hereditary Episodic Ataxias

    • Hereditary Episodic AtaxiaAutosomal dominant

      A group of dominantly inherited ataxias with attacks of imbalance, including EA1 (KCNA1), EA2 (CACNA1A) and EA6 (SLC1A3).

      • 1 GenCC submitter rates it definitive or strong
      What knowing changes

      Episodic ataxia type 2 often responds to acetazolamide or 4-aminopyridine, and avoiding known triggers can reduce attacks.

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.

      • 3 GenCC submitters rate it definitive or strong

  • Intellectual Disability

    • One of 233 genes linked to it

      • 1 GenCC submitter rates 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 SCN2A is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 2, with a bracket where SCN2A sits. SCN2A and 5 genes near it on chromosome 2, from 164,815,859 to 165,815,858.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 Mb165.2 Mb165.4 Mb165.6 Mb165.8 MbCOBLL1: 164,653,624–164,843,679, reverse strandCOBLL1SLC38A11: 164,894,354–164,955,632, reverse strandSLC38A11SCN3A: 165,087,516–165,204,093, reverse strandSCN3ASCN2A: 165,239,414–165,392,304, forward strandSCN2ACSRNP3: 165,469,647–165,689,407, forward strandCSRNP3GALNT3: 165,747,339–165,846,201, reverse strandGALNT3Diagram of SCN2A: 27 exons on the forward strand of chromosome 2Exon 2: 9 known disease-causing sitesExon 3: 3 known disease-causing sitesExon 4: 6 known disease-causing sitesExon 5: 6 known disease-causing sitesExon 6: 17 known disease-causing sitesExon 7: 23 known disease-causing sitesExon 8: 6 known disease-causing sitesExon 9: 14 known disease-causing sitesExon 10: 19 known disease-causing sitesExon 11: 11 known disease-causing sitesExon 12: 10 known disease-causing sitesExon 13: 1 known disease-causing siteExon 14: 12 known disease-causing sitesExon 15: 12 known disease-causing sitesExon 16: 38 known disease-causing sitesExon 17: 25 known disease-causing sitesExon 18: 1 known disease-causing siteExon 19: 8 known disease-causing sitesExon 20: 8 known disease-causing sitesExon 21: 9 known disease-causing sitesExon 22: 23 known disease-causing sitesExon 23: 5 known disease-causing sitesExon 24: 19 known disease-causing sitesExon 25: 23 known disease-causing sitesExon 26: 26 known disease-causing sitesExon 27: 70 known disease-causing sitesExon 1: 165,239,414–165,239,640, 227 basesExon 2: 165,295,773–165,296,090, 318 basesExon 3: 165,297,017–165,297,135, 119 basesExon 4: 165,307,848–165,307,937, 90 basesExon 5: 165,308,666–165,308,794, 129 basesExon 6: 165,309,352–165,309,443, 92 basesExon 7: 165,310,323–165,310,595, 273 basesExon 8: 165,312,025–165,312,088, 64 basesExon 9: 165,313,620–165,313,761, 142 basesExon 10: 165,313,902–165,314,108, 207 basesExon 11: 165,315,471–165,315,758, 288 basesExon 12: 165,323,156–165,323,500, 345 basesExon 13: 165,326,852–165,326,984, 133 basesExon 14: 165,331,330–165,331,568, 239 basesExon 15: 165,342,296–165,342,469, 174 basesExon 16: 165,344,555–165,344,911, 357 basesExon 17: 165,354,192–165,354,671, 480 basesExon 18: 165,365,143–165,365,263, 121 basesExon 19: 165,367,217–165,367,371, 155 basesExon 20: 165,370,126–165,370,299, 174 basesExon 21: 165,373,225–165,373,347, 123 basesExon 22: 165,374,685–165,374,966, 282 basesExon 23: 165,377,597–165,377,650, 54 basesExon 24: 165,380,592–165,380,729, 138 basesExon 25: 165,381,093–165,381,197, 105 basesExon 26: 165,386,746–165,387,016, 271 basesExon 27: 165,388,629–165,392,304, 3,676 bases1510152025275′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 8.8 kb of the gene's 152.9 kb; 6,018 of those bases code for the protein.

How a genome test reads SCN2A

433

positions in SCN2A where ClinVar classes a change as pathogenic or likely pathogenic

36 of them (8.3%) fall in regions short reads find hard.

  • Low mappability (36 sites)Regions where 100 bp or 250 bp reads cannot be placed uniquely.

A whole genome covers all 152.9 kb of SCN2A, introns included, not only the 8.8 kb of exons.

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.). SCN2A gene: sodium voltage-gated channel alpha subunit 2. Retrieved 17 October 2026, from https://dantelabs.com/genes/scn2a

Vancouver

Dante Labs. SCN2A gene: sodium voltage-gated channel alpha subunit 2 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/scn2a

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