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10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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SMPDL3A
sphingomyelin phosphodiesterase acid like 3A
Chromosome 6 · 6q22.31
NCBI Gene: 10924Ensembl: ENSG00000172594.14HGNC: HGNC:17389UniProt: Q92484
16PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
negative regulation of cGAS/STING signaling pathwayGO:0005615phosphoric diester hydrolase activityextracellular exosomealcohol drinkingtemporomandibular joint disorderidiopathic pulmonary fibrosisbreast disease
✦AI Summary

SMPDL3A is a secreted zinc-dependent phosphodiesterase that functions as a negative regulator of innate immunity 1. It catalyzes the linearization of 2',3'-cGAMP into 2'5'-bond pGpA and further hydrolyzes this product to generate GpA, thereby suppressing cGAS-STING signaling 1. Beyond cGAMP degradation, SMPDL3A exhibits in vitro nucleotide phosphodiesterase activity with nucleoside triphosphates (ATP) and diphosphates, with lower activity against nucleoside diphosphates and no activity against monophosphates 2. It also processes CDP-choline and CDP-ethanolamine but lacks sphingomyelin phosphodiesterase activity, despite structural homology to acid sphingomyelinase 2. Expression of SMPDL3A is upregulated by liver X receptor ligands and cholesterol loading in macrophages, linking lipid metabolism to immune regulation 23. N-glycosylation is essential for SMPDL3A stability, secretion, and enzymatic activity 4. In cancer contexts, SMPDL3A promotes hepatocellular carcinoma growth and metastasis through the LRPPRC pathway 5. The protein represents a critical intersection between cholesterol homeostasis and cGAS-STING-mediated inflammation 6.

Sources cited
1
SMPDL3A is a cGAMP-degrading enzyme that linearizes 2',3'-cGAMP and inhibits cGAS-STING signaling
PMID: 37890481
2
SMPDL3A is a nucleotide phosphodiesterase active against ATP and nucleotide diphosphates, upregulated by cholesterol loading in macrophages
PMID: 25288789
3
SMPDL3A is a liver X receptor-regulated gene in human blood cells
PMID: 22810003
4
N-glycosylation at specific sites is essential for SMPDL3A stability, secretion, and enzymatic activity
PMID: 28104755
5
SMPDL3A promotes hepatocellular carcinoma growth and metastasis via LRPPRC regulation
PMID: 39631618
6
SMPDL3A links cholesterol metabolism to cGAS-STING pathway regulation
PMID: 37967525
7
SMPDL3A is a di-zinc-dependent enzyme with substrate specificity for nucleotides
PMID: 26792860
Disease Associationsⓘ20
alcohol drinkingOpen Targets
0.30Weak
temporomandibular joint disorderOpen Targets
0.12Weak
idiopathic pulmonary fibrosisOpen Targets
0.12Weak
breast diseaseOpen Targets
0.11Weak
ocular hypotensionOpen Targets
0.08Suggestive
hepatocellular carcinomaOpen Targets
0.08Suggestive
neoplasmOpen Targets
0.07Suggestive
Romano-Ward syndromeOpen Targets
0.05Suggestive
catecholaminergic polymorphic ventricular tachycardiaOpen Targets
0.04Suggestive
Familial short QT syndromeOpen Targets
0.04Suggestive
Familial progressive cardiac conduction defectOpen Targets
0.04Suggestive
familial atrial fibrillationOpen Targets
0.04Suggestive
placenta praeviaOpen Targets
0.04Suggestive
Brugada syndromeOpen Targets
0.04Suggestive
familial sick sinus syndromeOpen Targets
0.04Suggestive
Wolff-Parkinson-White SyndromeOpen Targets
0.04Suggestive
atrial conduction diseaseOpen Targets
0.04Suggestive
hypertrophic cardiomyopathyOpen Targets
0.03Suggestive
hypertrophic cardiomyopathy 6Open Targets
0.03Suggestive
Rare familial disorder with hypertrophic cardiomyopathyOpen Targets
0.03Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
BRINP1Protein interaction98%PRF1Protein interaction73%ITPAShared pathway33%ENPP3Shared pathway29%DCTPP1Shared pathway25%LYPLAL1Shared pathway20%
Tissue Expression6 tissues
Liver
100%
Bone Marrow
84%
Lung
48%
Ovary
28%
Heart
18%
Brain
18%
Gene Interaction Network
Click a node to explore
SMPDL3ABRINP1PRF1ITPAENPP3DCTPP1LYPLAL1
PROTEIN STRUCTURE
Preparing viewer…
PDB5EBB · 2.60 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
1.29LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.94 [0.70–1.29]
RankingsWhere SMPDL3A stands among ~20K protein-coding genes
  • #15,393of 20,598
    Most Researched16
  • #13,587of 17,882
    Most Constrained (LOEUF)1.29
Genes detectedSMPDL3A
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Regulation of cGAS-STING signalling and its diversity of cellular outcomes.
PMID: 39774812
Nat Rev Immunol · 2025
1.00
2
Membrane integrity changes upon viral infection activate sphingomyelinase SMPDL3B to restrict cGAS-STING signaling via cGAMP degradation.
PMID: 41175872
Immunity · 2025
0.90
3
N-glycosylation of human sphingomyelin phosphodiesterase acid-like 3A (SMPDL3A) is essential for stability, secretion and activity.
PMID: 28104755
Biochem J · 2017
0.80
4
Sphingomyelin phosphodiesterase acid-like 3A (SMPDL3A) is a novel nucleotide phosphodiesterase regulated by cholesterol in human macrophages.
PMID: 25288789
J Biol Chem · 2014
0.70
5
METTL3-mediated SMPDL3A promotes cell growth, metastasis and immune process of hepatocellular carcinoma by regulating LRPPRC.
PMID: 39631618
Cell Signal · 2025
0.60