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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
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SPTSSA
serine palmitoyltransferase small subunit A
Chromosome 14 Β· 14q13.1
NCBI Gene: 171546Ensembl: ENSG00000165389.7HGNC: HGNC:20361UniProt: Q969W0
23PubMed Papers
22Diseases
0Drugs
2Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
endoplasmic reticulumserine C-palmitoyltransferase activityprotein bindingserine palmitoyltransferase complexspastic paraplegia 90A, autosomal dominantspastic paraplegia 90B, autosomal recessiveovarian neoplasmAlzheimer disease
✦AI Summary

SPTSSA (serine palmitoyltransferase small subunit A) is a regulatory component of the serine palmitoyltransferase (SPT) complex that catalyzes the rate-limiting step in sphingolipid biosynthesis 1. The SPT complex consists of catalytic subunits SPTLC1 and SPTLC2/SPTLC3, with SPTSSA serving as an activating small subunit that stimulates catalytic activity and determines substrate specificity 1. SPTSSA participates in acyl-CoA coordination, with different complex compositions showing distinct substrate preferences - the SPTLC1-SPTLC2-SPTSSA complex favors C16-CoA substrates while SPTLC1-SPTLC3-SPTSSA uses both C14-CoA and C16-CoA 2. The protein is subject to homeostatic regulation by ORMDL proteins that mediate feedback inhibition when sphingolipid levels become excessive 3. Pathogenic variants in SPTSSA cause hereditary spastic paraplegia by impairing ORMDL-mediated negative regulation, leading to excessive sphingolipid synthesis and neurological dysfunction 3. SPTSSA expression is also altered in various cancers, with upregulation associated with poor prognosis in gastric cancer and glioma 45, while decreased expression in renal cell carcinoma correlates with worse outcomes 6. Additionally, SPTSSA expression is affected by viral infections, potentially linking sphingolipid metabolism to immune responses 7.

Sources cited
1
SPTSSA is a component of the SPT complex that stimulates catalytic activity and regulates substrate specificity
PMID: 33558762
2
Different SPT complex compositions containing SPTSSA show distinct substrate preferences for acyl-CoA substrates
PMID: 39824719
3
Pathogenic SPTSSA variants cause hereditary spastic paraplegia by impairing ORMDL-mediated regulation and causing excessive sphingolipid synthesis
PMID: 36718090
4
SPTSSA overexpression promotes gastric cancer progression through Wnt/Ξ²-catenin pathway and PD-L1 modulation
PMID: 40498284
5
SPTSSA upregulation is associated with poor prognosis in glioma patients
PMID: 36062185
6
Decreased SPTSSA expression correlates with worse outcomes in clear cell renal cell carcinoma
PMID: 31512789
7
Viral infection affects SPTSSA expression in respiratory tract, linking sphingolipid metabolism to immune responses
PMID: 34851798
Disease Associationsβ“˜22
spastic paraplegia 90A, autosomal dominantOpen Targets
0.43Moderate
spastic paraplegia 90B, autosomal recessiveOpen Targets
0.38Weak
ovarian neoplasmOpen Targets
0.30Weak
Alzheimer diseaseOpen Targets
0.25Weak
neurodegenerative diseaseOpen Targets
0.25Weak
complex hereditary spastic paraplegiaOpen Targets
0.19Weak
open-angle glaucomaOpen Targets
0.16Weak
Abnormality of the skeletal systemOpen Targets
0.16Weak
glaucomaOpen Targets
0.14Weak
infectious meningitisOpen Targets
0.13Weak
diabetes mellitusOpen Targets
0.13Weak
gastric cancerOpen Targets
0.07Suggestive
maturity-onset diabetes of the young type 3Open Targets
0.04Suggestive
MODYOpen Targets
0.04Suggestive
hyperinsulinism due to INSR deficiencyOpen Targets
0.04Suggestive
3-hydroxy-3-methylglutaryl-CoA synthase deficiencyOpen Targets
0.04Suggestive
exercise-induced hyperinsulinismOpen Targets
0.04Suggestive
Glycogen storage disease due to hepatic glycogen synthase deficiencyOpen Targets
0.04Suggestive
glycogen storage disorder due to hepatic glycogen synthase deficiencyOpen Targets
0.04Suggestive
hyperproinsulinemiaOpen Targets
0.04Suggestive
Spastic paraplegia 90A, autosomal dominantUniProt
Spastic paraplegia 90B, autosomal recessiveUniProt
Pathogenic Variants2
NM_138288.4(SPTSSA):c.171_172del (p.Gln58fs)Pathogenic
Spastic paraplegia 90B, autosomal recessive
β˜†β˜†β˜†β˜†2025β†’ Residue 58
NM_138288.4(SPTSSA):c.152C>T (p.Thr51Ile)Pathogenic
Spastic paraplegia 90A, autosomal dominant
β˜†β˜†β˜†β˜†2025β†’ Residue 51
View on ClinVar β†—
Related Genes
ORMDL2Protein interaction100%ZDHHC9Protein interaction100%GOLGA7Protein interaction100%ORMDL1Protein interaction100%ORMDL3Protein interaction100%SPTLC1Protein interaction95%
Tissue Expression6 tissues
Lung
100%
Brain
86%
Liver
67%
Heart
48%
Ovary
46%
Bone Marrow
15%
Gene Interaction Network
Click a node to explore
SPTSSAORMDL2ZDHHC9GOLGA7ORMDL1ORMDL3SPTLC1
PROTEIN STRUCTURE
Preparing viewer…
PDB7K0K Β· 2.60 Γ… Β· EM
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
1.95LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF1.76 [0.88–1.95]
RankingsWhere SPTSSA stands among ~20K protein-coding genes
  • #13,529of 20,598
    Most Researched23
  • #4,545of 5,498
    Most Pathogenic Variants2
  • #17,682of 17,882
    Most Constrained (LOEUF)1.95
Genes detectedSPTSSA
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Sphingoid Base Diversity.
PMID: 39824719
Atherosclerosis Β· 2025
1.00
2
SPTSSA facilitates gastric cancer progression with modulating PD-L1 in immunomicroenvironment through Wnt/Ξ²-catenin pathway.
PMID: 40498284
Cell Oncol (Dordr) Β· 2025
0.90
3
Structural insights into the assembly and substrate selectivity of human SPT-ORMDL3 complex.
PMID: 33558762
Nat Struct Mol Biol Β· 2021
0.80
4
SPTSSA variants alter sphingolipid synthesis and cause a complex hereditary spastic paraplegia.
PMID: 36718090
Brain Β· 2023
0.70
5
PMID: 36062185
Oxid Med Cell Longev Β· 2022
0.60