SPTSSA

Chr 14q13.1

serine palmitoyltransferase small subunit A

Aliases:: ssSPTa
MANE:: ENST00000298130.5

OMIM: 613540 ↗NCBI: 171546 ↗Ensembl ↗

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Predicted protein structure

AlphaFold predicted structure

SPTSSA · Q969W0

v62025-08-01

Predicted Aligned Error matrix for SPTSSA — diagonal shows residue index, colour shows pairwise prediction confidence (lower is better) — Predicted Aligned Error

Mean pLDDT

93.6/ 100

Very high

71 residues

Confidence breakdown

Very high(≥ 90)90%
Confident(70–90)7%
Low(50–70)3%
Very low(< 50)0%

Open interactive 3D viewer

AlphaFold (Jumper et al., 2021) · CC BY 4.0

Clinical relevance (Genomics England PanelApp)

Diagnostic Grade (Green)

Childhood onset hereditary spastic paraplegia
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
DDG2P
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Disease associations (Open Targets)

spastic paraplegia 90A, autosomal dominant
0.65
spastic paraplegia 90B, autosomal recessive
0.38
ovarian neoplasm
0.29
neurodegenerative disease
0.25
Alzheimer disease
0.24
open-angle glaucoma
0.23
glaucoma
0.20
complex hereditary spastic paraplegia
0.19
Abnormality of the skeletal system
0.18
infectious meningitis
0.16

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

Protein function (UniProt)

Serine palmitoyltransferase small subunit A

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 (PubMed:19416851). The SPT complex is composed of SPTLC1, SPTLC2 or SPTLC3 and SPTSSA or SPTSSB. Within this complex, the heterodimer consisting of SPTLC1 and SPTLC2/SPTLC3 forms the catalytic core (PubMed:19416851). Within the SPT complex, SPTSSA stimulates the catalytic activity and plays a role in substrate specificity, which depends upon the overall complex composition (PubMed:19416851, PubMed:33558761). 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). Independently of its action as a SPT component, may be involved in MBOAT7 localization to mitochondria-associated membranes, a membrane bridge between the endoplasmic reticulum and mitochondria, may hence affect MBOAT7-catalyzed incorporation of arachidonic acid into phosphatidylinositol (PubMed:23510452)