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Gene

SCN11A

sodium voltage-gated channel alpha subunit 11

Summary

Cytogenetic location
3p22.2
Coordinates
Chromosome 3: 38,845,764–39,051,944 (GRCh38)
Exons
30 exons across 206.2 kb
Protein
1,791 amino acids
Also known as
Nav1.9, NaN, SNS-2
Previous symbols
SCN12A
MANE Select transcript
ENST00000302328.9NM_001349253.2
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 report relevant to this gene

  • Hereditary Sensory and Autonomic Neuropathies (incl. Familial Dysautonomia)

    • Hereditary Sensory and Autonomic Neuropathy

      A group of neuropathies, including familial dysautonomia (ELP1), HSAN1 (SPTLC1/SPTLC2), HSAN2 (WNK1, RETREG1) and congenital insensitivity to pain (NTRK1, SCN9A, PRDM12), most of which are recessive while HSAN1 is dominant.

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

      Protection against unnoticed injuries, burns and infections, management of autonomic symptoms, and carrier testing for relatives (familial dysautonomia is included in Ashkenazi Jewish carrier screening).

How SCN11A is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 3, with a bracket where SCN11A sits. SCN11A and 13 genes near it on chromosome 3, from 38,448,854 to 39,448,853.Chromosome 33p22.2p26.3p26.2p26.1p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p14.3p14.2p14.1p13p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13.11q13.12q13.13q13.2q13.31q13.32q13.33q21.1q21.2q21.3q22.1q22.2q22.3q23q24q25.1q25.2q25.31q25.32q25.33q26.1q26.2q26.31q26.32q26.33q27.1q27.2q27.3q28q2938.6 Mb38.8 Mb39 Mb39.2 Mb39.4 MbACVR2B: 38,453,843–38,493,142, forward strandACVR2BEXOG: 38,496,127–38,542,242, forward strandEXOGSCN5A: 38,548,057–38,649,743, reverse strandSCN5ASCN10A: 38,696,802–38,816,286, reverse strandSCN10ASCN11A: 38,845,764–39,051,944, reverse strandSCN11AWDR48: 39,051,991–39,096,671, forward strandWDR48GORASP1: 39,095,222–39,108,369, reverse strandGORASP1TTC21A: 39,107,194–39,140,973, forward strandTTC21ACSRNP1: 39,141,854–39,154,852, reverse strandCSRNP1XIRP1: 39,183,210–39,192,660, reverse strandXIRP1CX3CR1: 39,263,495–39,281,735, reverse strandCX3CR1CCR8: 39,329,709–39,336,269, forward strandCCR8SLC25A38: 39,383,292–39,397,426, forward strandSLC25A38RPSA: 39,406,709–39,426,255, forward strandRPSADiagram of SCN11A: 30 exons on the reverse strand of chromosome 3Exon 19: 1 known disease-causing siteExon 13: 1 known disease-causing siteExon 9: 3 known disease-causing sitesExon 5: 1 known disease-causing siteExon 30: 38,845,764–38,847,742, 1,979 basesExon 29: 38,850,481–38,850,751, 271 basesExon 28: 38,863,195–38,863,299, 105 basesExon 27: 38,867,321–38,867,458, 138 basesExon 26: 38,870,691–38,870,744, 54 basesExon 25: 38,871,445–38,871,708, 264 basesExon 24: 38,872,193–38,872,294, 102 basesExon 23: 38,879,950–38,880,123, 174 basesExon 22: 38,883,233–38,883,387, 155 basesExon 21: 38,885,288–38,885,402, 115 basesExon 20: 38,886,125–38,886,238, 114 basesExon 19: 38,894,533–38,894,964, 432 basesExon 18: 38,896,845–38,897,225, 381 basesExon 17: 38,899,894–38,900,073, 180 basesExon 16: 38,903,865–38,904,103, 239 basesExon 15: 38,905,192–38,905,321, 130 basesExon 14: 38,907,949–38,908,122, 174 basesExon 13: 38,908,997–38,909,194, 198 basesExon 12: 38,910,066–38,910,207, 142 basesExon 11: 38,919,935–38,920,001, 67 basesExon 10: 38,921,076–38,921,255, 180 basesExon 9: 38,925,415–38,925,509, 95 basesExon 8: 38,926,803–38,926,931, 129 basesExon 7: 38,945,411–38,945,512, 102 basesExon 6: 38,946,789–38,946,907, 119 basesExon 5: 38,950,096–38,950,369, 274 basesExon 4: 38,953,629–38,953,759, 131 basesExon 3: 38,960,283–38,960,423, 141 basesExon 2: 39,032,380–39,032,503, 124 basesExon 1: 39,051,861–39,051,944, 84 bases3025201510515′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 6.8 kb of the gene's 206.2 kb; 5,376 of those bases code for the protein.

How a genome test reads SCN11A

6

positions in SCN11A where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 206.2 kb of SCN11A, introns included, not only the 6.8 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.). SCN11A gene: sodium voltage-gated channel alpha subunit 11. Retrieved 16 October 2026, from https://dantelabs.com/genes/scn11a

Vancouver

Dante Labs. SCN11A gene: sodium voltage-gated channel alpha subunit 11 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/scn11a

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