NME3

Chr 16

NME/NM23 nucleoside diphosphate kinase 3

Also known as: DR-nm23, NDK3, NDPK-C, NDPKC, NM23-H3, NM23H3, c371H6.2

NCBI Gene: 4832ENSG00000103024UniProt: Q13232

Enables nucleoside diphosphate kinase activity. Involved in DNA repair; mitochondrial fusion; and nucleoside triphosphate biosynthetic process. Located in mitochondrial outer membrane. [provided by Alliance of Genome Resources, Jul 2025]

97
ClinVar variants
40
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— NME3
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
40 Pathogenic / Likely Pathogenic· 51 VUS of 97 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.
1.95LOEUF
pLI 0.000
Z-score -1.45
OE 1.68 (0.93–1.95)
Tolerant

Highly tolerant — LoF variants common in population

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.
-0.69Z-score
OE missense 1.21 (1.03–1.42)
106 obs / 87.9 exp
Tolerant

Tolerant to missense variation

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.1.68 (0.93–1.95)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.21 (1.03–1.42)
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.1.36
0≤1.21.6
LoF obs/exp: 9 / 5.4Missense obs/exp: 106 / 87.9Syn Z: -1.76

ClinVar Variant Classifications

97 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic39
Likely Pathogenic1
VUS51
Likely Benign3
Benign2
Conflicting1
39
Pathogenic
1
Likely Pathogenic
51
VUS
3
Likely Benign
2
Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
39
0
39
Likely Pathogenic
0
0
1
0
1
VUS
0
36
15
0
51
Likely Benign
0
0
2
1
3
Benign
0
1
1
0
2
Conflicting
—1
Total03758197

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

View in ClinVar →

Protein Context — Lollipop Plot

NME3 · 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
Nuclear functions of NME proteins.
Puts GS et al.·Lab Invest
2018Review
The nucleoside-diphosphate kinase NME3 associates with nephronophthisis proteins and is required for ciliary function during renal development.
Hoff S et al.·J Biol Chem
2018
Mitochondrial-related genes as prognostic and metastatic markers in breast cancer: insights from comprehensive analysis and clinical models.
Fang Y et al.·Front Immunol
2024Functional
Mitochondrial Probe for Glutathione Depletion Reveals NME3 Essentiality for Mitochondrial Redox Response.
Dhavarasa P et al.·ACS Chem Biol
2024
Elucidating prognostic significance of purine metabolism in colorectal cancer through integrating data from transcriptomic, immunohistochemical, and single-cell RNA sequencing analysis.
Kim S et al.·Mol Oncol
2025
[Expressing trend of NME3 protein in acute myeloid leukemia HL-60 cells and patients' bone marrow].
Wang WJ et al.·Zhongguo Shi Yan Xue Ye Xue Za Zhi
2013Cohort
Therapeutic Targeting of Non-oncogene Dependencies in High-risk Neuroblastoma.
Huang CT et al.·Clin Cancer Res
2019
Bcl3 selectively promotes metastasis of ERBB2-driven mammary tumors.
Wakefield A et al.·Cancer Res
2013
A Three-mRNA Signature Associated with Pyrimidine Metabolism for Prognosis of BRCA.
Zhang X et al.·Biomed Res Int
2022
Exome-based case-control association study using extreme phenotype design reveals novel candidates with protective effect in diabetic retinopathy.
Shtir C et al.·Hum Genet
2016
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