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10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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SMPD2
sphingomyelin phosphodiesterase 2
Chromosome 6 · 6q21
NCBI Gene: 6610Ensembl: ENSG00000135587.10HGNC: HGNC:11121UniProt: O60906
53PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
sphingomyelin phosphodiesterase activityprotein bindingsphingomyelin catabolic processphosphoric diester hydrolase activityAbnormality of the skeletal systemAlzheimer diseaseatrial fibrillationcancer
✦AI Summary

SMPD2 (sphingomyelin phosphodiesterase 2) is a neutral sphingomyelinase that catalyzes the hydrolysis of sphingomyelin to generate ceramide and phosphocholine 1. The enzyme also acts on alternative substrates including lyso-platelet-activating factor, lyso-phosphatidylcholine, and sphingosylphosphocholine 12. Structurally, SMPD2 forms dimers through C-terminal transmembrane helices, with the D111-K116 loop domain essential for substrate hydrolysis 3. In cancer biology, SMPD2 plays multifaceted roles in disease progression. Pan-cancer analysis demonstrates that SMPD2 expression correlates with tumor stage and clinical outcomes, with elevated expression associated with tumor immune evasion and dysfunctional T cell phenotypes 4. SMPD2 methylation status inversely correlates with mRNA expression and predicts immunotherapy response, showing superior predictive capacity for overall survival compared to established biomarkers 4. In hepatocellular carcinoma, SMPD2 enhances cell survival and migration, with silencing increasing sensitivity to lapatinib 5. Additionally, SMPD2 maintains sphingolipid metabolic balance in radiation-induced polyploid giant cancer cells, with lipid raft disruption impairing tumor repopulation and enhancing radiosensitivity 6. Beyond cancer, SMPD2 expression is upregulated by D-alanine in skin protection studies, enhancing skin barrier function and antioxidant defense 7. Hypermethylation of SMPD2 is associated with suicidal ideation in schizophrenia, suggesting epigenetic involvement in psychiatric disease 8.

Sources cited
1
SMPD2 catalyzes hydrolysis of sphingomyelin to ceramide and phosphocholine, and hydrolyzes lyso-platelet-activating factor
PMID: 10608884
2
SMPD2 acts on lyso-PC and sphingosylphosphocholine substrates
PMID: 14741383
3
SMPD2 structure reveals C-terminal transmembrane helices form dimeric architecture and D111-K116 loop is essential for substrate hydrolysis
PMID: 38012235
4
SMPD2 expression correlates with tumor stage, immune evasion, dysfunctional T cells, and predicts immunotherapy response superior to established biomarkers
PMID: 41021150
5
SMPD2 enhances survival and migration of hepatocellular carcinoma cells and silencing increases lapatinib sensitivity
PMID: 37006285
6
SMPD2 maintains sphingolipid metabolic balance in radiation-induced polyploid giant cancer cells; lipid raft disruption enhances radiosensitivity
PMID: 41330885
7
D-alanine upregulates SMPD2 gene expression as part of anti-aging skin protection effects
PMID: 40244537
8
SMPD2 distal promoter is hypermethylated in patients with suicidal ideation in schizophrenia
PMID: 32661777
Disease Associationsⓘ20
Abnormality of the skeletal systemOpen Targets
0.24Weak
Alzheimer diseaseOpen Targets
0.20Weak
atrial fibrillationOpen Targets
0.11Weak
cancerOpen Targets
0.08Suggestive
neoplasmOpen Targets
0.08Suggestive
clonal hematopoiesisOpen Targets
0.07Suggestive
lung carcinomaOpen Targets
0.06Suggestive
hepatocellular carcinomaOpen Targets
0.04Suggestive
melanomaOpen Targets
0.04Suggestive
pancreatic adenocarcinomaOpen Targets
0.02Suggestive
placenta praeviaOpen Targets
0.02Suggestive
coronary artery diseaseOpen Targets
0.02Suggestive
adrenal cortex carcinomaOpen Targets
0.02Suggestive
gliomaOpen Targets
0.02Suggestive
cutaneous melanomaOpen Targets
0.01Suggestive
oral squamous cell carcinomaOpen Targets
0.01Suggestive
colorectal cancerOpen Targets
0.01Suggestive
ovarian cancerOpen Targets
0.01Suggestive
heart failureOpen Targets
0.01Suggestive
infectionOpen Targets
0.01Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
NSMAFProtein interaction99%UGCGProtein interaction98%CERS2Protein interaction97%SGMS1Protein interaction97%ASAH1Protein interaction96%GALCProtein interaction96%
Tissue Expression6 tissues
Bone Marrow
100%
Lung
68%
Ovary
56%
Liver
48%
Brain
36%
Heart
29%
Gene Interaction Network
Click a node to explore
SMPD2NSMAFUGCGCERS2SGMS1ASAH1GALC
PROTEIN STRUCTURE
Preparing viewer…
PDB8J2F · 3.07 Å · EM
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
1.05LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.79 [0.61–1.05]
RankingsWhere SMPD2 stands among ~20K protein-coding genes
  • #8,498of 20,598
    Most Researched53
  • #10,448of 17,882
    Most Constrained (LOEUF)1.05
Genes detectedSMPD2
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
SMPD2 affects the prognosis of cancer patients by mediating lipid metabolism and the immune microenvironment.
PMID: 41021150
Discov Oncol · 2025
1.00
2
Skin Protection Effects of Lactobacillus paragasseri HN910 Lysate and the Role of Alanine.
PMID: 40244537
Probiotics Antimicrob Proteins · 2026
0.90
3
The Ceramide-Dependent EV Secretome Differentially Affects Prostate Cancer Cell Migration.
PMID: 40214501
Cells · 2025
0.80
4
Disrupting Lipid Raft Microdomains to Block Polyploid Giant Cancer Cell Budding and Enhance Radiotherapy Response.
PMID: 41330885
Adv Sci (Weinh) · 2026
0.70
5
Molecular basis for the catalytic mechanism of human neutral sphingomyelinases 1 (hSMPD2).
PMID: 38012235
Nat Commun · 2023
0.60