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Gene

SCN3A

sodium voltage-gated channel alpha subunit 3

Summary

Cytogenetic location
2q24.3
Coordinates
Chromosome 2: 165,087,526–165,204,050 (GRCh38)
Exons
28 exons across 116.5 kb
Protein
2,000 amino acids
Also known as
Nav1.3
MANE Select transcript
ENST00000283254.12NM_006922.4
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 report relevant to this gene

    • 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
        • 5 GenCC submitters rate it definitive or strong

    How SCN3A 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 SCN3A sits. SCN3A and 4 genes near it on chromosome 2, from 164,645,788 to 165,645,787.Chromosome 22q24.3p25.3p25.2p25.1p24.3p24.2p24.1p23.3p23.2p23.1p22.3p22.2p22.1p21p16.3p16.2p16.1p15p14p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13q14.1q14.2q14.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q34q35q36.1q36.2q36.3q37.1q37.2q37.3164.8 Mb165 Mb165.2 Mb165.4 Mb165.6 MbCOBLL1: 164,653,624–164,843,679, reverse strandCOBLL1SLC38A11: 164,894,354–164,955,632, reverse strandSLC38A11SCN3A: 165,087,526–165,204,050, reverse strandSCN3ASCN2A: 165,194,993–165,392,310, forward strandSCN2ACSRNP3: 165,469,647–165,689,407, forward strandCSRNP3Diagram of SCN3A: 28 exons on the reverse strand of chromosome 2Exon 28: 8 known disease-causing sitesExon 26: 3 known disease-causing sitesExon 25: 1 known disease-causing siteExon 23: 2 known disease-causing sitesExon 21: 1 known disease-causing siteExon 18: 1 known disease-causing siteExon 17: 2 known disease-causing sitesExon 16: 1 known disease-causing siteExon 13: 2 known disease-causing sitesExon 8: 1 known disease-causing siteExon 7: 1 known disease-causing siteExon 6: 1 known disease-causing siteExon 3: 1 known disease-causing siteExon 28: 165,087,526–165,091,345, 3,820 basesExon 27: 165,092,254–165,092,524, 271 basesExon 26: 165,094,374–165,094,478, 105 basesExon 25: 165,095,511–165,095,648, 138 basesExon 24: 165,096,467–165,096,520, 54 basesExon 23: 165,097,252–165,097,524, 273 basesExon 22: 165,100,302–165,100,424, 123 basesExon 21: 165,112,885–165,113,058, 174 basesExon 20: 165,113,816–165,113,970, 155 basesExon 19: 165,115,455–165,115,575, 121 basesExon 18: 165,127,631–165,128,101, 471 basesExon 17: 165,129,940–165,130,296, 357 bases. 1 variant with a page in exon 17. List themExon 16: 165,131,244–165,131,417, 174 basesExon 15: 165,137,879–165,138,117, 239 basesExon 14: 165,139,476–165,139,608, 133 basesExon 13: 165,140,651–165,140,998, 348 basesExon 12: 165,146,739–165,147,029, 291 basesExon 11: 165,154,452–165,154,658, 207 basesExon 10: 165,155,762–165,155,903, 142 basesExon 9: 165,162,308–165,162,371, 64 basesExon 8: 165,162,556–165,162,828, 273 basesExon 7: 165,163,618–165,163,709, 92 basesExon 6: 165,164,392–165,164,520, 129 bases. 1 variant with a page in exon 6. List themExon 5: 165,168,736–165,168,825, 90 basesExon 4: 165,170,430–165,170,548, 119 basesExon 3: 165,176,131–165,176,444, 314 basesExon 2: 165,186,551–165,186,747, 197 basesExon 1: 165,203,823–165,204,050, 228 bases2825201510515′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 9.1 kb of the gene's 116.5 kb; 6,003 of those bases code for the protein.

    How a genome test reads SCN3A

    29

    positions in SCN3A where ClinVar classes a change as pathogenic or likely pathogenic

    6 of them (21%) fall in regions short reads find hard.

    • Low mappability (6 sites)Regions where 100 bp or 250 bp reads cannot be placed uniquely.

    A whole genome covers all 116.5 kb of SCN3A, introns included, not only the 9.1 kb of exons.

    Variants with a page (2)

    The SCN3A 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
    F195Lfs*54c.585_586delExon 6165,164,407Pathogenic3 stars out of 4 reviewed by expert panel
    I875Tc.2624T>CExon 17165,130,238Pathogenic3 stars out of 4 reviewed by expert panel

    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.). SCN3A gene: sodium voltage-gated channel alpha subunit 3. Retrieved 17 October 2026, from https://dantelabs.com/genes/scn3a

    Vancouver

    Dante Labs. SCN3A gene: sodium voltage-gated channel alpha subunit 3 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/scn3a

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