EXD3

Chr 9

exonuclease 3'-5' domain containing 3

Also known as: Nbr, mut-7

NCBI Gene: 54932ENSG00000187609UniProt: Q8N9H8

Predicted to enable 3'-5' exonuclease activity; metal ion binding activity; and nucleic acid binding activity. Predicted to be involved in nucleobase-containing compound metabolic process. [provided by Alliance of Genome Resources, Jul 2025]

322
ClinVar variants
102
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— EXD3
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
102 Pathogenic / Likely Pathogenic· 199 VUS of 322 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.00LOEUF
pLI 0.000
Z-score 1.56
OE 0.74 (0.55–1.00)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.04Z-score
OE missense 0.99 (0.93–1.07)
535 obs / 537.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.74 (0.55–1.00)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.99 (0.93–1.07)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.97
0≤1.21.6
LoF obs/exp: 30 / 40.7Missense obs/exp: 535 / 537.7Syn Z: 0.33

ClinVar Variant Classifications

322 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic93
Likely Pathogenic9
VUS199
Likely Benign16
Benign1
Conflicting4
93
Pathogenic
9
Likely Pathogenic
199
VUS
16
Likely Benign
1
Benign
4
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
93
0
93
Likely Pathogenic
0
0
9
0
9
VUS
1
188
10
0
199
Likely Benign
0
14
1
1
16
Benign
0
1
0
0
1
Conflicting
—4
Total12031131322

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

EXD3 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Identification of Novel, Replicable Genetic Risk Loci for Suicidal Thoughts and Behaviors Among US Military Veterans.
Kimbrel NA et al.·JAMA Psychiatry
2023Meta-analysis
Genome-wide association study identifies four pan-ancestry loci for suicidal ideation in the Million Veteran Program.
Ashley-Koch AE et al.·PLoS Genet
2023Meta-analysis
A genome-wide association study identifies genetic variants associated with hip pain in the UK Biobank cohort (N = 221,127).
Pan Q et al.·Sci Rep
2025Cohort
Modelling G protein-biased agonism using GLP-1 receptor C-terminal mutations.
Tran HD et al.·Mol Metab
2026Functional
Is famine exposure during developmental life in rural Bangladesh associated with a metabolic and epigenetic signature in young adulthood? A historical cohort study.
Finer S et al.·BMJ Open
2016Cohort
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools