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Gene

SPTLC1

serine palmitoyltransferase long chain base subunit 1

Summary

Cytogenetic location
9q22.31
Coordinates
Chromosome 9: 92,031,147–92,115,413 (GRCh38)
Exons
15 exons across 84.3 kb
Protein
473 amino acids
Also known as
LCB1, SPTI, HSAN1, hLCB1
Previous symbols
HSN1
MANE Select transcript
ENST00000262554.7NM_006415.4
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

  • Amyotrophic Lateral Sclerosis (ALS)

    • Amyotrophic Lateral Sclerosis

      A neurodegenerative disorder of upper and lower motor neurons, occurring in sporadic and familial forms.

      • 3 GenCC submitters rate it definitive or strong
      What knowing changes

      Tofersen (Qalsody, FDA 2023) for SOD1-ALS; ASO trials for C9orf72 and FUS; riluzole; edaravone; AMX0035 (sodium phenylbutyrate-taurursodiol); multidisciplinary ALS clinic care; respiratory support; genetic counseling for family members

  • 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
      • 3 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 SPTLC1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 9, with a bracket where SPTLC1 sits. SPTLC1 and 8 genes near it on chromosome 9, from 91,573,280 to 92,573,279.Chromosome 99q22.31p24.3p24.2p24.1p23p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q13q21.11q21.12q21.13q21.2q21.31q21.32q21.33q22.1q22.2q22.31q22.32q22.33q31.1q31.2q31.3q32q33.1q33.2q33.3q34.11q34.12q34.13q34.2q34.391.6 Mb91.8 Mb92 Mb92.2 Mb92.4 MbROR2: 91,563,091–91,950,278, reverse strandROR2SPTLC1: 92,031,147–92,115,413, reverse strandSPTLC1IARS1: 92,210,199–92,293,854, reverse strandIARS1NOL8: 92,297,358–92,325,636, reverse strandNOL8CENPP: 92,325,625–92,620,529, forward strandCENPPOGN: 92,383,268–92,406,734, reverse strandOGNOMD: 92,412,034–92,424,481, reverse strandOMDASPN: 92,456,193–92,492,208, reverse strandASPNECM2: 92,493,554–92,536,736, reverse strandECM2Diagram of SPTLC1: 15 exons on the reverse strand of chromosome 9Exon 11: 5 known disease-causing sitesExon 6: 1 known disease-causing siteExon 5: 2 known disease-causing sitesExon 2: 4 known disease-causing sitesExon 15: 92,031,147–92,032,558, 1,412 basesExon 14: 92,034,810–92,034,883, 74 basesExon 13: 92,038,248–92,038,365, 118 basesExon 12: 92,045,999–92,046,053, 55 basesExon 11: 92,047,172–92,047,268, 97 basesExon 10: 92,047,613–92,047,708, 96 basesExon 9: 92,049,960–92,050,067, 108 basesExon 8: 92,055,405–92,055,494, 90 basesExon 7: 92,059,179–92,059,308, 130 basesExon 6: 92,067,966–92,068,098, 133 basesExon 5: 92,080,016–92,080,088, 73 basesExon 4: 92,080,870–92,080,963, 94 basesExon 3: 92,108,740–92,108,834, 95 basesExon 2: 92,112,455–92,112,562, 108 basesExon 1: 92,115,314–92,115,413, 100 bases1510515′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 2.8 kb of the gene's 84.3 kb; 1,422 of those bases code for the protein.

How a genome test reads SPTLC1

12

positions in SPTLC1 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 84.3 kb of SPTLC1, introns included, not only the 2.8 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.). SPTLC1 gene: serine palmitoyltransferase long chain base subunit 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/sptlc1

Vancouver

Dante Labs. SPTLC1 gene: serine palmitoyltransferase long chain base subunit 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/sptlc1

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