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GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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EXD3
exonuclease 3'-5' domain containing 3
Chromosome 9 · 9q34.3
NCBI Gene: 54932Ensembl: ENSG00000187609.17HGNC: HGNC:26023UniProt: Q8N9H8
13PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
protein bindingnucleic acid binding3'-5' exonuclease activityBack painpolycystic ovary syndromehypertensionresponse to xenobiotic stimulus
✦AI Summary

EXD3 (exonuclease 3'-5' domain containing 3) is a nuclease enzyme that possesses 3'-5' exoribonuclease activity and is required for 3'-end trimming of AGO1-bound miRNAs. The protein demonstrates AP (apurinic/apyrimidinic) endonuclease activity, capable of incising DNA backbone at AP sites and performing exonucleolytic digestion on nicked AP sites 1. EXD3 appears to function in DNA damage response pathways, specifically involved in recovery from replication stress-induced cell cycle arrest 1. In kidney biology, EXD3 plays a functional role in podocyte integrity, with knockdown studies showing reduced nephrin gene expression in cultured human podocytes 2. Disease associations include diabetic kidney disease, where a rare missense variant (p.Asp555Asn) shows strong association with disease risk (OR=8.7) and EXD3 is downregulated in affected kidney tissue 2. The gene has also been implicated in psychiatric conditions, with genetic variants associated with suicidal ideation and behaviors 34. Additionally, EXD3 shows differential exon usage in TDP-43 proteinopathy models relevant to ALS/FTD 5, and variants are associated with hip pain 6 and gastric cancer progression 7. These findings suggest EXD3 functions in multiple biological processes including RNA processing, DNA repair, and cellular stress responses.

Sources cited
1
EXD3 possesses AP endonuclease activity and is involved in recovery from replication stress-induced cell cycle arrest
PMID: 41183359
2
EXD3 plays a role in podocyte integrity, with rare variants strongly associated with diabetic kidney disease risk
PMID: 41541775
3
EXD3 variants are associated with suicidal ideation in genome-wide association studies
PMID: 36940203
4
EXD3 variants are associated with suicidal thoughts and behaviors in US military veterans
PMID: 36515925
5
EXD3 shows differential exon usage in TDP-43 proteinopathy models relevant to ALS/FTD
PMID: 35946434
6
EXD3 variants are associated with hip pain in genome-wide association studies
PMID: 39843573
7
EXD3 is upregulated in gastric cancer and associated with poorer prognosis
PMID: 30890511
Disease Associationsⓘ20
Back painOpen Targets
0.37Weak
polycystic ovary syndromeOpen Targets
0.25Weak
hypertensionOpen Targets
0.23Weak
response to xenobiotic stimulusOpen Targets
0.21Weak
Limb painOpen Targets
0.20Weak
Sleep DisorderOpen Targets
0.16Weak
Abdominal painOpen Targets
0.16Weak
HeadacheOpen Targets
0.16Weak
mathematical abilityOpen Targets
0.15Weak
suicide behaviourOpen Targets
0.15Weak
Abnormality of the skeletal systemOpen Targets
0.15Weak
suicidal ideationOpen Targets
0.14Weak
chronic musculoskeletal painOpen Targets
0.14Weak
circadian rhythmOpen Targets
0.14Weak
anxiety disorderOpen Targets
0.12Weak
major depressive disorderOpen Targets
0.11Weak
Abnormal urine sodium concentrationOpen Targets
0.10Weak
musculoskeletal system diseaseOpen Targets
0.10Suggestive
alcohol drinkingOpen Targets
0.10Suggestive
restless legs syndromeOpen Targets
0.08Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
ZFYVE28Protein interaction71%
Tissue Expression6 tissues
Ovary
100%
Lung
73%
Liver
62%
Bone Marrow
30%
Heart
30%
Brain
19%
Gene Interaction Network
Click a node to explore
EXD3ZFYVE28
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q8N9H8
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
1.37LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF1.15 [0.96–1.37]
RankingsWhere EXD3 stands among ~20K protein-coding genes
  • #16,156of 20,598
    Most Researched13
  • #14,319of 17,882
    Most Constrained (LOEUF)1.37
Genes detectedEXD3
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Effects of urban living environments on mental health in adults.
PMID: 37322117
Nat Med · 2023
1.00
2
Identification of Novel, Replicable Genetic Risk Loci for Suicidal Thoughts and Behaviors Among US Military Veterans.
PMID: 36515925
JAMA Psychiatry · 2023
0.90
3
[Bioinformatics analysis of expression and function of EXD3 gene in gastric cancer].
PMID: 30890511
Nan Fang Yi Ke Da Xue Xue Bao · 2019
0.80
4
Genome-wide association study identifies four pan-ancestry loci for suicidal ideation in the Million Veteran Program.
PMID: 36940203
PLoS Genet · 2023
0.70
5
Exome-Wide Analysis Identifies a Rare
PMID: 41541775
Kidney Int Rep · 2026
0.60