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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
SPTLC2
serine palmitoyltransferase long chain base subunit 2
Chromosome 14 Β· 14q24.3
NCBI Gene: 9517Ensembl: ENSG00000100596.9HGNC: HGNC:11278UniProt: O15270
97PubMed Papers
21Diseases
0Drugs
10Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
sphingolipid biosynthetic processceramide biosynthetic processpositive regulation of lipophagyserine C-palmitoyltransferase activityhereditary sensory and autonomic neuropathy type 1neurodegenerative diseaseCharcot-Marie-Tooth diseaseRiley-Day syndrome
✦AI Summary

SPTLC2 encodes a catalytic subunit of serine palmitoyltransferase (SPT), the rate-limiting enzyme in de novo sphingolipid biosynthesis 1. The enzyme catalyzes condensation of L-serine and acyl-CoA to form long-chain bases, with SPTLC1-SPTLC2 heterodimers showing strong preference for C16-CoA substrates 2. SPTLC2 expression is upregulated in hepatocytes during metabolic dysfunction-associated steatohepatitis (MASH), where it drives pathogenic ceramide accumulation 3. In brain ischemia, SPTLC2 promotes ceramide production in astrocytes, triggering mitochondrial permeabilization, mtDNA release, and neuroinflammation through cGAS/STING signaling 4. The enzyme incorporates trans-fatty acids preferentially into sphingolipids, contributing to atherosclerotic cardiovascular disease through altered lipoprotein trafficking 2. Gain-of-function mutations in SPTLC2 cause juvenile amyotrophic lateral sclerosis by disrupting SPT regulation and increasing ceramide levels 5. Therapeutically, SPTLC2 knockdown reduces ceramide synthesis and ameliorates both brain ischemic injury and MASH progression 43. The enzyme also responds to nicotinamide treatment, enhancing ceramide biosynthesis to improve epidermal barrier function 6.

Sources cited
1
SPTLC2 encodes a catalytic subunit of SPT that catalyzes de novo sphingolipid biosynthesis
PMID: 32788725
2
SPTLC1-SPTLC2 heterodimers show substrate preference for C16-CoA and incorporate trans-fatty acids into sphingolipids
PMID: 39547233
3
SPTLC2 is upregulated in hepatocytes during MASH and drives pathogenic ceramide accumulation
PMID: 41004573
4
SPTLC2 promotes ceramide production in brain ischemia, triggering neuroinflammation through mitochondrial dysfunction
PMID: 39956315
5
Gain-of-function SPTLC2 mutations cause juvenile ALS by increasing ceramide levels
PMID: 38041684
6
Nicotinamide enhances SPTLC2-mediated ceramide biosynthesis for epidermal barrier function
PMID: 10971324
Disease Associationsβ“˜21
hereditary sensory and autonomic neuropathy type 1Open Targets
0.70Moderate
neurodegenerative diseaseOpen Targets
0.56Moderate
Charcot-Marie-Tooth diseaseOpen Targets
0.49Moderate
Familial dysautonomiaOpen Targets
0.46Moderate
Riley-Day syndromeOpen Targets
0.46Moderate
amyotrophic lateral sclerosisOpen Targets
0.39Weak
Alzheimer diseaseOpen Targets
0.38Weak
hereditary sensory and autonomic neuropathyOpen Targets
0.37Weak
Parkinson diseaseOpen Targets
0.37Weak
multiple sclerosisOpen Targets
0.37Weak
hereditary sensory neuropathy-deafness-dementia syndromeOpen Targets
0.37Weak
lysosomal storage diseaseOpen Targets
0.37Weak
neuroinflammatory disorderOpen Targets
0.37Weak
genetic disorderOpen Targets
0.34Weak
cervical carcinomaOpen Targets
0.29Weak
VitiligoOpen Targets
0.27Weak
central nervous system cancerOpen Targets
0.19Weak
joint diseaseOpen Targets
0.18Weak
nephrotic syndromeOpen Targets
0.16Weak
Peyronie diseaseOpen Targets
0.15Weak
Neuropathy, hereditary sensory and autonomic, 1CUniProt
Pathogenic Variants10
NM_004863.4(SPTLC2):c.547C>T (p.Arg183Trp)Pathogenic
Neuropathy, hereditary sensory and autonomic, type 1C|Inborn genetic diseases|not provided|Hereditary neuropathy or pain disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 183
NM_004863.4(SPTLC2):c.1151C>T (p.Ser384Phe)Pathogenic
Charcot-Marie-Tooth disease|Neuropathy, hereditary sensory and autonomic, type 1C|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 384
NM_004863.4(SPTLC2):c.1145G>T (p.Gly382Val)Pathogenic
Neuropathy, hereditary sensory and autonomic, type 1C|not provided
β˜…β˜…β˜†β˜†2020β†’ Residue 382
NM_004863.4(SPTLC2):c.544G>C (p.Ala182Pro)Pathogenic
Neuropathy, hereditary sensory and autonomic, type 1C
β˜…β˜†β˜†β˜†2026β†’ Residue 182
NM_004863.4(SPTLC2):c.1144G>C (p.Gly382Arg)Likely pathogenic
Neuropathy, hereditary sensory and autonomic, type 1C
β˜…β˜†β˜†β˜†2025β†’ Residue 382
NM_004863.4(SPTLC2):c.131A>G (p.Gln44Arg)Pathogenic
Neuropathy, hereditary sensory and autonomic, type 1C
β˜…β˜†β˜†β˜†2024β†’ Residue 44
NM_004863.4(SPTLC2):c.545C>T (p.Ala182Val)Likely pathogenic
Neuropathy, hereditary sensory and autonomic, type 1C
β˜…β˜†β˜†β˜†2022β†’ Residue 182
NM_004863.4(SPTLC2):c.1148C>T (p.Ala383Val)Pathogenic
not provided
β˜…β˜†β˜†β˜†2021β†’ Residue 383
NM_004863.4(SPTLC2):c.640G>A (p.Asp214Asn)Pathogenic
Hypercholesterolemia, familial, 1
β˜†β˜†β˜†β˜†2022β†’ Residue 214
NM_004863.4(SPTLC2):c.1510A>T (p.Ile504Phe)Pathogenic
NEUROPATHY, HEREDITARY SENSORY AND AUTONOMIC, TYPE IC, SEVERE
β˜†β˜†β˜†β˜†2010β†’ Residue 504
View on ClinVar β†—
Related Genes
ORMDL3Protein interaction100%ACER2Protein interaction97%ACER1Protein interaction97%DEGS2Protein interaction95%ORMDL1Protein interaction95%ORMDL2Protein interaction95%
Tissue Expression6 tissues
Brain
100%
Bone Marrow
62%
Lung
42%
Heart
36%
Ovary
25%
Liver
16%
Gene Interaction Network
Click a node to explore
SPTLC2ORMDL3ACER2ACER1DEGS2ORMDL1ORMDL2
PROTEIN STRUCTURE
Preparing viewer…
PDB7K0K Β· 2.60 Γ… Β· EM
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.49Moderately Constrained
pLIβ“˜
0.98Intolerant
Observed/Expected LoF0.34 [0.24–0.49]
RankingsWhere SPTLC2 stands among ~20K protein-coding genes
  • #4,969of 20,598
    Most Researched97 Β· top quartile
  • #2,846of 5,498
    Most Pathogenic Variants10
  • #2,930of 17,882
    Most Constrained (LOEUF)0.49 Β· top quartile
Genes detectedSPTLC2
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
A 20-year Clinical and Genetic Neuromuscular Cohort Analysis in Lebanon: An International Effort.
PMID: 34602496
J Neuromuscul Dis Β· 2022
1.00
2
Serine restriction alters sphingolipid diversity to constrain tumour growth.
PMID: 32788725
Nature Β· 2020
0.90
3
Ceramides increase mitochondrial permeabilization to trigger mtDNA-dependent inflammation in astrocytes during brain ischemia.
PMID: 39956315
Metabolism Β· 2025
0.80
4
Targeted inhibition of hepatic de novo ceramide synthesis ameliorates MASH.
PMID: 41004573
Sci Adv Β· 2025
0.70
5
Altered sphingolipid biosynthetic flux and lipoprotein trafficking contribute to trans-fat-induced atherosclerosis.
PMID: 39547233
Cell Metab Β· 2025
0.60