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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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SMPD4
sphingomyelin phosphodiesterase 4
Chromosome 2 Β· 2q21.1
NCBI Gene: 55627Ensembl: ENSG00000136699.20HGNC: HGNC:32949UniProt: A0A7P0TB24
88PubMed Papers
1Diseases
0Drugs
29Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
Golgi apparatusnuclear outer membraneendoplasmic reticulumtrans-Golgi networkNeurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies
✦AI Summary

SMPD4 encodes a neutral sphingomyelinase that catalyzes hydrolysis of sphingomyelin to phosphorylcholine and ceramide 1. This enzyme localizes to endoplasmic reticulum and nuclear envelope membranes, where it maintains sphingolipid homeostasis and membrane integrity 1. SMPD4 interacts with nuclear pore complex components, particularly nucleoporin NUP35, suggesting involvement in nuclear envelope dynamics and nuclear pore insertion 2. Biallelic loss-of-function variants in SMPD4 cause severe neurodevelopmental disorder characterized by progressive congenital microcephaly, arthrogryposis, and structural brain anomalies including hypomyelination and cerebellar hypoplasia 314. Mechanistically, SMPD4 deficiency impairs neural progenitor proliferation, causes prolonged mitosis, and abnormal nuclear envelope breakdown during cell division 1. In neural stem cells, SMPD4 loss results in reduced proliferation and shortened primary cilia, defects rescued by exogenous ceramide supplementation 5. Affected individuals surviving beyond infancy frequently develop insulin-dependent diabetes, making SMPD4-related disease a multisystem disorder 1. Conversely, elevated SMPD4 expression in hepatocellular carcinoma associates with poor prognosis and promotes tumor cell proliferation, invasion, and migration 6, indicating distinct roles in normal development versus pathological proliferation.

Sources cited
1
SMPD4 catalyzes sphingomyelin hydrolysis to ceramide, localizes to ER and nuclear envelope, interacts with NPCs, and biallelic loss-of-function causes congenital microcephaly and diabetes with defective nuclear envelope dynamics and progenitor proliferation
PMID: 36732302
2
SMPD4 variants identified in patients with arthrogryposis and fetal akinesia as a recently identified gene for arthrogryposis with brain malformations
PMID: 33060286
3
SMPD4 deletion causes neurodevelopmental disorder with arthrogryposis, microcephaly, hypomyelination, simplified gyral pattern, and corpus callosum hypoplasia
PMID: 34621002
4
SMPD4 associates with nucleoporin components including NUP35 near ER and nuclear membrane, suggesting role in nuclear pore membrane dynamics
PMID: 35203325
5
SMPD4-produced ceramide is essential for primary cilia development and brain development; SMPD4 deficiency causes neural progenitor death, shortened cilia, and cerebellar hypoplasia
PMID: 39470011
6
High SMPD4 expression in hepatocellular carcinoma associates with poor prognosis and promotes tumor cell proliferation, invasion, and migration
PMID: 40211349
Disease Associationsβ“˜1
Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomaliesUniProt
Pathogenic Variants29
NM_017951.5(SMPD4):c.1290-9G>APathogenic
Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies|not provided
β˜…β˜…β˜†β˜†2025
NM_017951.5(SMPD4):c.784_785del (p.Leu262fs)Pathogenic
Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies
β˜…β˜…β˜†β˜†2025β†’ Residue 262
NM_017951.5(SMPD4):c.345+1G>TPathogenic
Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies|Hepatocellular carcinoma
β˜…β˜…β˜†β˜†2023
NM_017951.5(SMPD4):c.525_550dup (p.Tyr184fs)Likely pathogenic
Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies
β˜…β˜†β˜†β˜†2025β†’ Residue 184
NM_017951.5(SMPD4):c.1612C>T (p.Gln538Ter)Likely pathogenic
Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies
β˜…β˜†β˜†β˜†2024β†’ Residue 538
NM_017951.5(SMPD4):c.273_289del (p.Pro92fs)Likely pathogenic
Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies
β˜…β˜†β˜†β˜†2024β†’ Residue 92
NM_017951.5(SMPD4):c.1504C>T (p.Arg502Ter)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 502
NM_017951.5(SMPD4):c.1971del (p.Asp658fs)Likely pathogenic
Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies
β˜…β˜†β˜†β˜†2024β†’ Residue 658
NM_017951.5(SMPD4):c.1660-28_1666delLikely pathogenic
Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies
β˜…β˜†β˜†β˜†2024
NM_017951.5(SMPD4):c.127-2A>GLikely pathogenic
Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies
β˜…β˜†β˜†β˜†2024
NM_017951.5(SMPD4):c.2068del (p.Asp690fs)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 690
NM_017951.5(SMPD4):c.2063del (p.Gln688fs)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 688
NM_017951.5(SMPD4):c.1098-2A>GLikely pathogenic
Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies
β˜…β˜†β˜†β˜†2022
NM_017951.5(SMPD4):c.1487del (p.Ile496fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2022β†’ Residue 496
NM_017951.5(SMPD4):c.546_547del (p.Ala183fs)Likely pathogenic
Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies
β˜…β˜†β˜†β˜†2022β†’ Residue 183
NM_017951.5(SMPD4):c.792+2T>GPathogenic
Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies
β˜…β˜†β˜†β˜†2022
NM_017951.5(SMPD4):c.2074G>T (p.Glu692Ter)Likely pathogenic
Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies
β˜…β˜†β˜†β˜†2022β†’ Residue 692
NM_017951.5(SMPD4):c.-67_-66delPathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2022
NM_017951.5(SMPD4):c.1961_1962delinsC (p.Lys654fs)Likely pathogenic
Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies
β˜…β˜†β˜†β˜†2022β†’ Residue 654
NM_017951.5(SMPD4):c.270-1G>APathogenic
Neurodevelopmental disorder with microcephaly, arthrogryposis, and structural brain anomalies
β˜…β˜†β˜†β˜†2021
View on ClinVar β†—
Related Genes
PLPP2Protein interaction100%PLPP3Protein interaction100%ASAH2Protein interaction98%ACER2Protein interaction97%ACER1Protein interaction97%CERS6Protein interaction97%
Tissue Expression

No tissue expression data available for this gene.

Gene Interaction Network
Click a node to explore
SMPD4PLPP2PLPP3ASAH2ACER2ACER1CERS6
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q9NXE4
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.77LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.62 [0.50–0.77]
RankingsWhere SMPD4 stands among ~20K protein-coding genes
  • #5,444of 20,598
    Most Researched88
  • #1,844of 5,498
    Most Pathogenic Variants29
  • #6,226of 17,882
    Most Constrained (LOEUF)0.77
Genes detectedSMPD4
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
Neurogenetic fetal akinesia and arthrogryposis: genetics, expanding genotype-phenotypes and functional genomics.
PMID: 33060286
J Med Genet Β· 2021
0.90
3
SMPD4 regulates mitotic nuclear envelope dynamics and its loss causes microcephaly and diabetes.
PMID: 36732302
Brain Β· 2023
0.80
4
Growth and neurodevelopmental disorder with arthrogryposis, microcephaly and structural brain anomalies caused by Bi-allelic partial deletion of SMPD4 gene.
PMID: 34621002
J Hum Genet Β· 2022
0.70
5
High expression of SMPD4 promotes liver cancer and is associated with poor prognosis.
PMID: 40211349
BMC Res Notes Β· 2025
0.60