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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.
SMPD1
sphingomyelin phosphodiesterase 1
Chromosome 11 Β· 11p15.4
NCBI Gene: 6609Ensembl: ENSG00000166311.11HGNC: HGNC:11120UniProt: E9LUE8
194PubMed Papers
22Diseases
0Drugs
385Pathogenic Variants
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
sphingomyelin phosphodiesterase activityprotein bindingzinc ion bindingpositive regulation of endocytosisNiemann-Pick disease type ANiemann-Pick disease type BNiemann-Pick diseaseacid sphingomyelinase deficiency
✦AI Summary

SMPD1 encodes sphingomyelin phosphodiesterase 1 (acid sphingomyelinase), a lysosomal enzyme catalyzing sphingomyelin hydrolysis to ceramide and phosphocholine 1. Loss-of-function SMPD1 mutations cause acid sphingomyelinase deficiency (ASMD), presenting as Niemann-Pick disease types A and Bβ€”autosomal recessive lysosomal storage disorders with distinct severity profiles 2. Type A manifests neuronopathic features with visceral involvement and premature death, while type B presents primarily visceral manifestations including hepatosplenomegaly and pulmonary disease 3. Biochemically, ASMD patients show decreased peripheral leukocyte acid sphingomyelinase activity and elevated plasma 7-ketocholesterol levels correlating with disease severity 3. Genotype-phenotype correlations identify specific variants associated with disease onset and progression; for example, p.Arg602His and p.Asn522Ser homozygotes exhibit late-onset type B, while p.His284SerfsX18 and related variants correlate with neuronopathic type A 3. Beyond inherited disease, SMPD1 inhibition shows therapeutic potential in glioblastoma and hepatocellular carcinoma through ceramide pathway modulation and lysosomal dysfunction induction 41. Additionally, SMPD1 variants contribute to Parkinson's disease genetic burden, implicating lysosomal dysfunction in neurodegeneration 5. Enzyme replacement therapy with olipudase Ξ± represents the first approved disease-modifying treatment for ASMD patients 2.

Sources cited
1
SMPD1 catalyzes sphingomyelin hydrolysis to ceramide and phosphocholine; inhibition causes lysosomal damage and cell death
PMID: 37211762
2
SMPD1 mutations cause acid sphingomyelinase deficiency in Niemann-Pick types A and B; olipudase Ξ± is approved enzyme replacement therapy
PMID: 38397448
3
Decreased acid sphingomyelinase activity and elevated 7-ketocholesterol correlate with NPA/B disease severity; specific SMPD1 variants associate with clinical phenotypes
PMID: 33675270
4
SMPD1 inhibition by fluoxetine kills glioblastoma cells through EGFR signaling inhibition and lysosomal stress activation
PMID: 34731610
5
SMPD1 variants contribute to Parkinson's disease genetic burden, implicating lysosomal dysfunction in neurodegeneration
PMID: 29140481
6
SMPD1 deficiency causes Niemann-Pick disease A and B, autosomal recessive lysosomal storage disorders with visceral and neurologic symptoms
PMID: 37003582
Disease Associationsβ“˜22
Niemann-Pick disease type AOpen Targets
0.86Strong
Niemann-Pick disease type BOpen Targets
0.85Strong
Niemann-Pick diseaseOpen Targets
0.67Moderate
acid sphingomyelinase deficiencyOpen Targets
0.60Moderate
lysosomal storage diseaseOpen Targets
0.58Moderate
Alzheimer diseaseOpen Targets
0.54Moderate
Parkinson diseaseOpen Targets
0.54Moderate
neurodegenerative diseaseOpen Targets
0.53Moderate
multiple sclerosisOpen Targets
0.52Moderate
genetic disorderOpen Targets
0.47Moderate
Niemann-Pick disease, type C1Open Targets
0.43Moderate
Intellectual disabilityOpen Targets
0.38Weak
neuronal ceroid lipofuscinosisOpen Targets
0.33Weak
ceroid lipofuscinosis, neuronal, 6AOpen Targets
0.33Weak
Abnormality of metabolism/homeostasisOpen Targets
0.27Weak
Gaucher diseaseOpen Targets
0.11Weak
neoplasmOpen Targets
0.11Weak
SepsisOpen Targets
0.10Weak
melanomaOpen Targets
0.10Weak
non-alcoholic steatohepatitisOpen Targets
0.08Suggestive
Niemann-Pick disease AUniProt
Niemann-Pick disease BUniProt
Pathogenic Variants385
NM_000543.5(SMPD1):c.973C>G (p.Pro325Ala)Pathogenic
Niemann-Pick disease, type A;Niemann-Pick disease, type B|Niemann-Pick disease, type A
β˜…β˜…β˜†β˜†2026β†’ Residue 325
NM_000543.5(SMPD1):c.667T>G (p.Cys223Gly)Likely pathogenic
Niemann-Pick disease, type A;Niemann-Pick disease, type B
β˜…β˜…β˜†β˜†2026β†’ Residue 223
NM_000543.5(SMPD1):c.354del (p.Ile119fs)Pathogenic
not provided|Niemann-Pick disease, type A|Niemann-Pick disease, type B;Niemann-Pick disease, type A
β˜…β˜…β˜†β˜†2026β†’ Residue 119
NM_000543.5(SMPD1):c.757G>C (p.Asp253His)Pathogenic
Niemann-Pick disease, type A|not provided|Niemann-Pick disease, type B;Niemann-Pick disease, type A|Niemann-Pick disease, type B|Sphingomyelin/cholesterol lipidosis|SMPD1-related disorder
β˜…β˜…β˜†β˜†2026β†’ Residue 253
NM_000543.5(SMPD1):c.7del (p.Arg3fs)Pathogenic
Niemann-Pick disease, type A|Niemann-Pick disease, type B;Niemann-Pick disease, type A|Sphingomyelin/cholesterol lipidosis
β˜…β˜…β˜†β˜†2026β†’ Residue 3
NM_000543.5(SMPD1):c.1327C>T (p.Arg443Ter)Pathogenic
Niemann-Pick disease, type B|Niemann-Pick disease, type A|not provided|Niemann-Pick disease, type B;Niemann-Pick disease, type A|not specified|Sphingomyelin/cholesterol lipidosis
β˜…β˜…β˜†β˜†2026β†’ Residue 443
NM_000543.5(SMPD1):c.1624C>T (p.Arg542Ter)Pathogenic
not provided|Niemann-Pick disease, type B;Niemann-Pick disease, type A|Niemann-Pick disease, type B|Niemann-Pick disease, type A|Sphingomyelin/cholesterol lipidosis|See cases|Niemann-Pick disease, type C1|Acid sphingomyelinase deficiency
β˜…β˜…β˜†β˜†2026β†’ Residue 542
NM_000543.5(SMPD1):c.175del (p.Ala59fs)Pathogenic
Niemann-Pick disease, type A;Niemann-Pick disease, type B|Niemann-Pick disease, type A
β˜…β˜…β˜†β˜†2026β†’ Residue 59
NM_000543.5(SMPD1):c.1276G>A (p.Gly426Ser)Pathogenic
not provided|Niemann-Pick disease, type A|Niemann-Pick disease, type B;Niemann-Pick disease, type A|Niemann-Pick disease, type B|Sphingomyelin/cholesterol lipidosis
β˜…β˜…β˜†β˜†2026β†’ Residue 426
NM_000543.5(SMPD1):c.730G>A (p.Gly244Arg)Pathogenic
Niemann-Pick disease, type B|not provided|Sphingomyelin/cholesterol lipidosis|Niemann-Pick disease, type B;Niemann-Pick disease, type A|Niemann-Pick disease, type A
β˜…β˜…β˜†β˜†2026β†’ Residue 244
NM_000543.5(SMPD1):c.1735G>A (p.Gly579Ser)Pathogenic
Niemann-Pick disease, type A|Sphingomyelin/cholesterol lipidosis|Niemann-Pick disease, type B;Niemann-Pick disease, type A
β˜…β˜…β˜†β˜†2026β†’ Residue 579
NM_000543.5(SMPD1):c.1054G>T (p.Glu352Ter)Pathogenic
Niemann-Pick disease, type B;Niemann-Pick disease, type A|Niemann-Pick disease, type A|Sphingomyelin/cholesterol lipidosis|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 352
NM_000543.5(SMPD1):c.996del (p.Phe333fs)Pathogenic
Niemann-Pick disease, type A|Sphingomyelin/cholesterol lipidosis|not provided|Niemann-Pick disease, type B|Niemann-Pick disease, type B;Niemann-Pick disease, type A|Acid sphingomyelinase deficiency
β˜…β˜…β˜†β˜†2026β†’ Residue 333
NM_000543.5(SMPD1):c.28C>T (p.Gln10Ter)Pathogenic
Niemann-Pick disease, type A|Niemann-Pick disease, type B;Niemann-Pick disease, type A|SMPD1-related disorder
β˜…β˜…β˜†β˜†2026β†’ Residue 10
NM_000543.5(SMPD1):c.955G>C (p.Gly319Arg)Pathogenic
Niemann-Pick disease, type A|Niemann-Pick disease, type B|Niemann-Pick disease, type B;Niemann-Pick disease, type A
β˜…β˜…β˜†β˜†2025β†’ Residue 319
NM_000543.5(SMPD1):c.1092-1G>CPathogenic
not provided|Niemann-Pick disease, type A|Niemann-Pick disease, type A;Niemann-Pick disease, type B
β˜…β˜…β˜†β˜†2025
NM_000543.5(SMPD1):c.1565A>G (p.Asn522Ser)Pathogenic
Niemann-Pick disease, type A|Niemann-Pick disease, type A;Niemann-Pick disease, type B|Niemann-Pick disease, type B
β˜…β˜…β˜†β˜†2025β†’ Residue 522
NM_000543.5(SMPD1):c.1804C>T (p.Arg602Cys)Likely pathogenic
Niemann-Pick disease, type A;Niemann-Pick disease, type B|Sphingomyelin/cholesterol lipidosis|Niemann-Pick disease, type A
β˜…β˜…β˜†β˜†2025β†’ Residue 602
NM_000543.5(SMPD1):c.911T>C (p.Leu304Pro)Pathogenic
Niemann-Pick disease, type A|Sphingomyelin/cholesterol lipidosis|not provided|Niemann-Pick disease, type B|Niemann-Pick disease, type B;Niemann-Pick disease, type A
β˜…β˜…β˜†β˜†2025β†’ Residue 304
NM_000543.5(SMPD1):c.1267C>T (p.His423Tyr)Pathogenic
Niemann-Pick disease, type B|Sphingomyelin/cholesterol lipidosis|Niemann-Pick disease, type A|Niemann-Pick disease, type B;Niemann-Pick disease, type A|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 423
View on ClinVar β†—
Related Genes
UGCGProtein interaction98%ASAH2Protein interaction98%ACER2Protein interaction97%ACER1Protein interaction97%CERS6Protein interaction97%GBA1Protein interaction97%
Tissue Expression6 tissues
Liver
100%
Heart
71%
Lung
56%
Brain
33%
Ovary
28%
Bone Marrow
16%
Gene Interaction Network
Click a node to explore
SMPD1UGCGASAH2ACER2ACER1CERS6GBA1
PROTEIN STRUCTURE
Preparing viewer…
PDB5I81 Β· 2.25 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
1.06LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.83 [0.66–1.06]
RankingsWhere SMPD1 stands among ~20K protein-coding genes
  • #2,208of 20,598
    Most Researched194 Β· top quartile
  • #146of 5,498
    Most Pathogenic Variants385 Β· top 5%
  • #10,605of 17,882
    Most Constrained (LOEUF)1.06
Genes detectedSMPD1
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
The Niemann-Pick type diseases - A synopsis of inborn errors in sphingolipid and cholesterol metabolism.
PMID: 37003582
Prog Lipid Res Β· 2023
1.00
2
Targeting glioblastoma signaling and metabolism with a re-purposed brain-penetrant drug.
PMID: 34731610
Cell Rep Β· 2021
0.90
3
Clinical, biochemical, and genotype-phenotype correlations of 118 patients with Niemann-Pick disease Types A/B.
PMID: 33675270
Hum Mutat Β· 2021
0.80
4
Excessive burden of lysosomal storage disorder gene variants in Parkinson's disease.
PMID: 29140481
Brain Β· 2017
0.70
5
Polyphyllin D punctures hypertrophic lysosomes to reverse drug resistance of hepatocellular carcinoma by targeting acid sphingomyelinase.
PMID: 37211762
Mol Ther Β· 2023
0.60