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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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PLD3
phospholipase D family member 3
Chromosome 19 · 19q13.2
NCBI Gene: 23646Ensembl: ENSG00000105223.22HGNC: HGNC:17158UniProt: Q8IV08
117PubMed Papers
21Diseases
0Drugs
1Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
endoplasmic reticulum membraneearly endosome membranelate endosome membraneextracellular exosomeAutosomal dominant cerebellar ataxia type 1neurodegenerative diseaseAlzheimer diseaseprostate cancer
✦AI Summary

PLD3 (phospholipase D family member 3) functions as a 5'→3' single-stranded DNA and RNA exonuclease that regulates endosomal nucleic acid sensing and immune responses 1. The protein degrades single-stranded nucleic acids in endolysosomal compartments, processing self and pathogenic DNA/RNA molecules that could serve as danger signals for innate immune receptors like toll-like receptors (TLRs) 1. PLD3 works cooperatively with endonuclease RNase T2 to generate specific RNA ligands for TLR7 activation, releasing 2',3'-cyclic guanosine monophosphate and cytidine-rich RNA fragments that trigger antiviral immune responses 2. Additionally, PLD3 functions as a transphosphatidylase that synthesizes (S,S)-bis(monoacylglycero)phosphate (BMP), a crucial lysosomal phospholipid required for lipid degradation, particularly gangliosides 3. The protein regulates endolysosomal homeostasis and impacts cellular removal of dysfunctional organelles via autophagy 3. Clinically, PLD3 is associated with spinocerebellar ataxia 46 and has been identified as a risk factor for late-onset Alzheimer's disease through rare coding variants 45. PLD3 expression is downregulated in Alzheimer's disease brains, negatively correlating with amyloid precursor protein and amyloid-β levels 5.

Sources cited
1
PLD3 functions as a 5' exonuclease that breaks down TLR9 ligands and regulates inflammatory cytokine responses
PMID: 30111894
2
PLD3 cooperates with RNase T2 to generate RNA ligands for TLR7 activation and antiviral immunity
PMID: 38697119
3
PLD3 synthesizes lysosomal S,S-BMP phospholipid required for ganglioside degradation
PMID: 39423811
4
PLD3 coding variants are associated with increased Alzheimer's disease risk
PMID: 24951455
5
PLD3 expression is downregulated in AD brains and negatively correlates with APP and Aβ levels
PMID: 24935720
Disease Associationsⓘ21
Autosomal dominant cerebellar ataxia type 1Open Targets
0.25Weak
neurodegenerative diseaseOpen Targets
0.17Weak
Alzheimer diseaseOpen Targets
0.14Weak
Familial prostate cancerOpen Targets
0.11Weak
prostate cancerOpen Targets
0.11Weak
Blackfan-Diamond anemiaOpen Targets
0.08Suggestive
breast cancerOpen Targets
0.07Suggestive
ThrombocytopeniaOpen Targets
0.07Suggestive
atherosclerosisOpen Targets
0.07Suggestive
hereditary persistence of fetal hemoglobin-sickle cell disease syndromeOpen Targets
0.07Suggestive
Hereditary persistence of fetal hemoglobin - beta-thalassemiaOpen Targets
0.07Suggestive
inosine triphosphatase deficiencyOpen Targets
0.06Suggestive
Beta-thalassemia - X-linked thrombocytopeniaOpen Targets
0.06Suggestive
beta-thalassemia-X-linked thrombocytopenia syndromeOpen Targets
0.06Suggestive
alpha thalassemia-intellectual disability syndrome type 1Open Targets
0.06Suggestive
Alpha-thalassemia - intellectual disability syndrome linked to chromosome 16Open Targets
0.06Suggestive
Alpha-thalassemia - myelodysplastic syndromeOpen Targets
0.06Suggestive
alpha-thalassemia-myelodysplastic syndromeOpen Targets
0.06Suggestive
autosomal dominant macrothrombocytopeniaOpen Targets
0.06Suggestive
macrothrombocytopenia, isolated, 2, autosomal dominantOpen Targets
0.06Suggestive
Spinocerebellar ataxia 46UniProt
Pathogenic Variants1
NC_000019.10:g.40394766delPathogenic
Spinocerebellar ataxia 46
★☆☆☆2019
View on ClinVar ↗
Related Genes
PISDProtein interaction98%CDS1Protein interaction97%DGKGProtein interaction97%CDS2Protein interaction97%PLA2G12AProtein interaction96%PTDSS2Protein interaction96%
Tissue Expression6 tissues
Ovary
100%
Lung
88%
Brain
81%
Liver
63%
Heart
60%
Bone Marrow
32%
Gene Interaction Network
Click a node to explore
PLD3PISDCDS1DGKGCDS2PLA2G12APTDSS2
PROTEIN STRUCTURE
Preparing viewer…
PDB8Q1K · 1.51 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.73LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.54 [0.40–0.73]
RankingsWhere PLD3 stands among ~20K protein-coding genes
  • #4,060of 20,598
    Most Researched117 · top quartile
  • #4,841of 5,498
    Most Pathogenic Variants1
  • #5,640of 17,882
    Most Constrained (LOEUF)0.73
Genes detectedPLD3
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Alzheimer's disease risk genes and mechanisms of disease pathogenesis.
PMID: 24951455
Biol Psychiatry · 2015
1.00
2
Identification of novel therapeutic targets for chronic kidney disease and kidney function by integrating multi-omics proteome with transcriptome.
PMID: 38898508
Genome Med · 2024
0.90
3
Autosomal dominant cerebellar ataxias: new genes and progress towards treatments.
PMID: 37479376
Lancet Neurol · 2023
0.80
4
PLD3 and PLD4 synthesize S,S-BMP, a key phospholipid enabling lipid degradation in lysosomes.
PMID: 39423811
Cell · 2024
0.70
5
Midline assembloids reveal regulators of human axon guidance.
PMID: 40674484
Science · 2025
0.60