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Gene

SPTLC2

serine palmitoyltransferase long chain base subunit 2

Summary

Cytogenetic location
14q24.3
Coordinates
Chromosome 14: 77,505,997–77,616,637 (GRCh38)
Exons
12 exons across 110.6 kb
Protein
562 amino acids
Also known as
KIAA0526, LCB2, LCB2A, hLCB2a
MANE Select transcript
ENST00000216484.7NM_004863.4
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.

      • ClinGen rates the link strong
      • 1 GenCC submitter rates 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
      • 5 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 SPTLC2 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 14, with a bracket where SPTLC2 sits. SPTLC2 and 17 genes near it on chromosome 14, from 77,061,317 to 78,061,316.Chromosome 1414q24.3p13p12p11.2p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.11q32.12q32.13q32.2q32.31q32.32q32.3377.2 Mb77.4 Mb77.6 Mb77.8 Mb78 MbCIPC: 77,098,126–77,117,287, forward strandCIPC: 77,098,311–77,225,462, forward strandTMEM63C: 77,116,568–77,259,498, forward strandTMEM63CZDHHC22: 77,131,266–77,143,032, reverse strandZDHHC22NGB: 77,265,483–77,271,211, reverse strandNGBPOMT2: 77,274,956–77,320,898, reverse strandPOMT2GSTZ1: 77,320,996–77,344,021, forward strandGSTZ1TMED8: 77,335,024–77,377,348, reverse strandTMED8SAMD15: 77,376,689–77,392,372, forward strandSAMD15NOXRED1: 77,394,021–77,423,523, reverse strandNOXRED1VIPAS39: 77,426,674–77,457,952, reverse strandVIPAS39AHSA1: 77,457,743–77,469,482, forward strandAHSA1ISM2: 77,474,394–77,499,408, reverse strandISM2SPTLC2: 77,505,997–77,616,637, reverse strandSPTLC2ALKBH1: 77,672,401–77,708,038, reverse strandALKBH1SLIRP: 77,708,045–77,761,104, forward strandSLIRPSNW1: 77,709,019–77,761,207, reverse strandSNW1ADCK1: 77,800,059–77,937,188, forward strandADCK1Diagram of SPTLC2: 12 exons on the reverse strand of chromosome 14Exon 8: 3 known disease-causing sitesExon 4: 4 known disease-causing sitesExon 1: 1 known disease-causing siteExon 12: 77,505,997–77,512,403, 6,407 basesExon 11: 77,518,038–77,518,167, 130 basesExon 10: 77,521,446–77,521,581, 136 basesExon 9: 77,552,096–77,552,222, 127 basesExon 8: 77,555,300–77,555,519, 220 basesExon 7: 77,557,041–77,557,146, 106 basesExon 6: 77,562,396–77,562,489, 94 basesExon 5: 77,570,384–77,570,508, 125 basesExon 4: 77,576,767–77,576,915, 149 basesExon 3: 77,578,955–77,579,109, 155 basesExon 2: 77,597,186–77,597,380, 195 basesExon 1: 77,616,448–77,616,637, 190 bases1210864215′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 kb of the gene's 110.6 kb; 1,689 of those bases code for the protein.

How a genome test reads SPTLC2

8

positions in SPTLC2 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 110.6 kb of SPTLC2, introns included, not only the 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.). SPTLC2 gene: serine palmitoyltransferase long chain base subunit 2. Retrieved 17 October 2026, from https://dantelabs.com/genes/sptlc2

Vancouver

Dante Labs. SPTLC2 gene: serine palmitoyltransferase long chain base subunit 2 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/sptlc2

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