Skip to content
GenoLensGenoLens

SPTLC1

Chr 9q22.31

serine palmitoyltransferase long chain base subunit 1

Aliases:
LCB1, SPTI, HSAN1, hLCB1
MANE:
ENST00000262554.7
OMIM: 605712 ↗NCBI: 10558 ↗Ensembl ↗

Annotations refreshed 1 month ago.

Predicted protein structure

Clinical relevance (Genomics England PanelApp)

Diagnostic Grade (Green)

  • Adult onset neurodegenerative disorder

    MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

  • Familial dysautonomia

    MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

  • Hereditary neuropathy

    MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

  • Hereditary neuropathy or pain disorder

    MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

  • Likely inborn error of metabolism

    MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

  • Pain syndromes

    MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

  • Undiagnosed metabolic disorders

    MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

  • Retinal disorders

    MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

+3 more panels — install the extension to see the full list inline on any page.

Disease associations (Open Targets)

  • neuropathy, hereditary sensory and autonomic, type 1A

    0.70

  • hereditary sensory and autonomic neuropathy type 1

    0.67

  • amyotrophic lateral sclerosis 27, juvenile

    0.63

  • Charcot-Marie-Tooth disease

    0.58

  • Familial dysautonomia

    0.46

  • hereditary sensory and autonomic neuropathy type 2

    0.46

  • Riley-Day syndrome

    0.46

  • hereditary disease

    0.45

  • juvenile amyotrophic lateral sclerosis

    0.39

  • neurodegenerative disease

    0.35

Score is the Open Targets composite evidence score (0-1). Higher = stronger gene-disease association.

Protein function (UniProt)

Serine palmitoyltransferase 1

Component of the serine palmitoyltransferase multisubunit enzyme (SPT) that catalyzes the initial and rate-limiting step in sphingolipid biosynthesis by condensing L-serine and activated acyl-CoA (most commonly palmitoyl-CoA) to form long-chain bases. The SPT complex is also composed of SPTLC2 or SPTLC3 and SPTSSA or SPTSSB. Within this complex, the heterodimer with SPTLC2 or SPTLC3 forms the catalytic core (PubMed:19416851, PubMed:33558762, PubMed:36170811). The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference (PubMed:19416851, PubMed:33558762). The SPTLC1-SPTLC2-SPTSSA complex shows a strong preference for C16-CoA substrate, while the SPTLC1-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as substrates, with a slight preference for C14-CoA (PubMed:19416851, PubMed:19648650). The SPTLC1-SPTLC2-SPTSSB complex shows a strong preference for C18-CoA substrate, while the SPTLC1-SPTLC3-SPTSSB isozyme displays an ability to use a broader range of acyl-CoAs, without apparent preference (PubMed:19416851, PubMed:19648650, PubMed:33558761, PubMed:33558762). Required for adipocyte cell viability and metabolic homeostasis (By similarity)

Diseases associated with SPTLC1

Curated MONDO disease pages that list SPTLC1 among their top associated genes.

Data sources: HGNC (CC BY 4.0), AlphaFold (CC BY 4.0, Jumper et al. Nature 2021), Genomics England PanelApp (CC BY 4.0), ClinGen, Open Targets (CC0), UniProt.

Not for sole clinical decision-making. Always verify against primary sources.