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10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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SPTLC3
serine palmitoyltransferase long chain base subunit 3
Chromosome 20 · 20p12.1
NCBI Gene: 55304Ensembl: ENSG00000172296.14HGNC: HGNC:16253UniProt: Q9NUV7
33PubMed Papers
20Diseases
0Drugs
1Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
sphingoid biosynthetic processserine C-palmitoyltransferase activityprotein bindingserine palmitoyltransferase complexalcohol drinkingcholelithiasismale reproductive organ cancerperipheral neuropathy
✦AI Summary

SPTLC3 (serine palmitoyltransferase long chain base subunit 3) is a specialized catalytic component of the serine palmitoyltransferase (SPT) enzyme complex that determines substrate specificity in sphingolipid biosynthesis 1. Unlike the ubiquitously expressed SPTLC1 and SPTLC2 subunits, SPTLC3 shows restricted tissue expression and generates structurally distinct sphingolipids with shorter chain lengths 2. The SPTLC1-SPTLC3 heterodimer produces C16-sphinganine and C16-sphingosine, creating approximately 15% of human plasma sphingolipids, while also utilizing C14-CoA substrates more efficiently than SPTLC2-containing complexes 1. SPTLC3 expression is induced under pathological conditions, particularly in ischemic cardiomyopathy where it is transcriptionally regulated by HIF1α and contributes to mitochondrial complex I dysfunction, oxidative stress, and cardiac dysfunction 3. The enzyme also plays roles in metabolic diseases, with genetic variants like rs364585 associated with altered serum lipid profiles 4. SPTLC3 is notably expressed in specific tissues like urinary bladder epithelium, where it contributes to phytoceramide production important for membrane properties 5. Its dysregulation has been implicated in cardiovascular disease progression through altered sphingolipid metabolism and lipoprotein trafficking 6.

Sources cited
1
SPTLC3 generates C16-sphinganine and C16-sphingosine, constituting ~15% of human plasma sphingolipids
PMID: 19648650
2
SPTLC3 has restricted tissue expression and is associated with cardio-metabolic diseases
PMID: 35503173
3
SPTLC3 is induced in ischemic cardiomyopathy by HIF1α and affects mitochondrial complex I function
PMID: 38660786
4
SPTLC3 rs364585 polymorphism is associated with serum lipid profile variations
PMID: 28056980
5
SPTLC3 is expressed in urinary bladder epithelium and contributes to phytoceramide production
PMID: 36441023
6
SPTLC3 contributes to atherosclerosis through altered sphingolipid metabolism and lipoprotein trafficking
PMID: 39547233
Disease Associationsⓘ20
alcohol drinkingOpen Targets
0.41Moderate
cholelithiasisOpen Targets
0.36Weak
male reproductive organ cancerOpen Targets
0.31Weak
peripheral neuropathyOpen Targets
0.27Weak
Sensory neuropathyOpen Targets
0.27Weak
biliary tract diseaseOpen Targets
0.26Weak
ankylosing spondylitisOpen Targets
0.25Weak
ovarian dysfunctionOpen Targets
0.24Weak
systemic lupus erythematosusOpen Targets
0.21Weak
Moyamoya diseaseOpen Targets
0.20Weak
hyperaldosteronismOpen Targets
0.19Weak
stomach diseaseOpen Targets
0.18Weak
liver diseaseOpen Targets
0.17Weak
male reproductive system diseaseOpen Targets
0.17Weak
retinitis pigmentosaOpen Targets
0.07Suggestive
early-onset non-syndromic cataractOpen Targets
0.06Suggestive
hepatocellular carcinomaOpen Targets
0.06Suggestive
Familial exudative vitreoretinopathyOpen Targets
0.06Suggestive
Familial ocular anterior segment mesenchymal dysgenesisOpen Targets
0.05Suggestive
Posterior polar cataractOpen Targets
0.05Suggestive
Pathogenic Variants1
NM_018327.4(SPTLC3):c.448T>C (p.Trp150Arg)Likely pathogenic
Peripheral neuropathy;Sensory neuropathy
★☆☆☆2015→ Residue 150
View on ClinVar ↗
Related Genes
ORMDL3Protein interaction100%ORMDL1Protein interaction95%AGXTProtein interaction94%CBSProtein interaction94%GDF1Protein interaction94%ORM1Protein interaction94%
Tissue Expression6 tissues
Liver
100%
Heart
50%
Ovary
37%
Lung
22%
Brain
7%
Bone Marrow
6%
Gene Interaction Network
Click a node to explore
SPTLC3ORMDL3ORMDL1AGXTCBSGDF1ORM1
PROTEIN STRUCTURE
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AlphaFoldAI-predicted · UniProt Q9NUV7
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.86LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.65 [0.50–0.86]
RankingsWhere SPTLC3 stands among ~20K protein-coding genes
  • #11,426of 20,598
    Most Researched33
  • #5,241of 5,498
    Most Pathogenic Variants1
  • #7,543of 17,882
    Most Constrained (LOEUF)0.86
Genes detectedSPTLC3
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Sphingoid Base Diversity.
PMID: 39824719
Atherosclerosis · 2025
1.00
2
Altered sphingolipid biosynthetic flux and lipoprotein trafficking contribute to trans-fat-induced atherosclerosis.
PMID: 39547233
Cell Metab · 2025
0.90
3
SPTLC3 Is Essential for Complex I Activity and Contributes to Ischemic Cardiomyopathy.
PMID: 38660786
Circulation · 2024
0.80
4
Serine Palmitoyltransferase Subunit 3 and Metabolic Diseases.
PMID: 35503173
Adv Exp Med Biol · 2022
0.70
5
The SPTLC3 subunit of serine palmitoyltransferase generates short chain sphingoid bases.
PMID: 19648650
J Biol Chem · 2009
0.60