NUDT3

Chr 6

nudix hydrolase 3

Also known as: DIPP, DIPP-1, DIPP1

NCBI Gene: 11165ENSG00000272325UniProt: O95989

NUDT3 belongs to the MutT, or Nudix, protein family. Nudix proteins act as homeostatic checkpoints at important stages in nucleoside phosphate metabolic pathways, guarding against elevated levels of potentially dangerous intermediates, like 8-oxo-dGTP, which promotes AT-to-CG transversions (Safrany et al., 1998 [PubMed 9822604]).[supplied by OMIM, Feb 2011]

15
ClinVar variants
4
Pathogenic / LP
0.43
pLI score
0
Active trials
Clinical Summary— NUDT3
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.21) despite low pLI — interpret in context.
📋
ClinVar Variants
4 Pathogenic / Likely Pathogenic· 11 VUS of 15 total submissions
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

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.
0.66LOEUF
pLI 0.425
Z-score 2.27
OE 0.21 (0.08–0.66)
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.
1.32Z-score
OE missense 0.63 (0.51–0.78)
63 obs / 100.1 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.0.21 (0.08–0.66)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.63 (0.51–0.78)
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.1.26
0≤1.21.6
LoF obs/exp: 2 / 9.6Missense obs/exp: 63 / 100.1Syn Z: -1.27

ClinVar Variant Classifications

15 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic4
VUS11
4
Pathogenic
11
VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
4
0
4
Likely Pathogenic
0
0
0
0
0
VUS
0
7
4
0
11
Likely Benign
0
0
0
0
0
Benign
0
0
0
0
0
Total078015

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

View in ClinVar →

Protein Context — Lollipop Plot

NUDT3 · protein map & ClinVar variants

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

OMIM — Genotype-Phenotype

OMIM

No OMIM entries found.

Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
The Obesity-Linked Gene Nudt3 Drosophila Homolog Aps Is Associated With Insulin Signaling.
Williams MJ et al.·Mol Endocrinol
2015
Nudt3 is an mRNA decapping enzyme that modulates cell migration.
Grudzien-Nogalska E et al.·RNA
2016
Disentangling the genetics of sarcopenia: prioritization of NUDT3 and KLF5 as genes for lean mass & HLA-DQB1-AS1 for hand grip strength with the associated enhancing SNPs & a scoring system.
Singh AN et al.·BMC Med Genet
2020
Integrative Role of RNA N7-methylguanosine in epilepsy: Regulation of neuronal oxidative phosphorylation, programmed death and immune microenvironment.
Zhao J et al.·PLoS One
2025
A comprehensive analysis of m6A/m7G/m5C/m1A-related gene expression and immune infiltration in liver ischemia-reperfusion injury by integrating bioinformatics and machine learning algorithms.
Meng Z et al.·Eur J Med Res
2024
A novel long non-coding RNA, PICSAR, promotes thyroid cancer progression through the hsa-miR-320A/hsa-miR-485/RAPGEFL1 axis.
Hejazi M et al.·Med Oncol
2025
Genetic polymorphisms associated with pediatric-onset type 2 diabetes: A family-based transmission disequilibrium test and case-control study.
Miranda-Lora AL et al.·Pediatr Diabetes
2019
Construction of N-7 methylguanine-related mRNA prognostic model in uterine corpus endometrial carcinoma based on multi-omics data and immune-related analysis.
Zhao J et al.·Sci Rep
2022Functional
A high throughput, functional screen of human Body Mass Index GWAS loci using tissue-specific RNAi Drosophila melanogaster crosses.
Baranski TJ et al.·PLoS Genet
2018Functional
Blood Transcriptomics Identifies Multiple Gene Expression Pathways Associated with the Clinical Efficacy of Hymenoptera Venom Immunotherapy.
Demšar Luzar A et al.·Int J Mol Sci
2024
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