NSUN3

Chr 3AR

NOP2/Sun RNA methyltransferase 3

Also known as: COXPD48, MST077, MSTP077

NCBI Gene: 63899ENSG00000178694UniProt: Q9H649OMIM: 617491

NSUN3 encodes a mitochondrial tRNA methyltransferase that methylates cytosine at the wobble position of mitochondrial tRNA(Met), enabling recognition of both AUG and AUA codons during mitochondrial protein synthesis. Mutations cause combined oxidative phosphorylation deficiency 48, a mitochondrial disorder affecting cellular energy production. The condition follows autosomal recessive inheritance.

OMIMResearchSummary from RefSeq, OMIM, UniProt
ARLOEUF 1.291 OMIM phenotype
Clinical Summary— NSUN3
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
16 unique Pathogenic / Likely Pathogenic· 97 VUS of 165 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.29LOEUF
pLI 0.000
Z-score 0.67
OE 0.82 (0.54–1.29)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.31Z-score
OE missense 0.93 (0.82–1.06)
164 obs / 175.4 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.82 (0.54–1.29)
0≤0.351.4
Missense OE0.93 (0.82–1.06)
0≤0.61.4
Synonymous OE0.86
0≤1.21.6
LoF obs/exp: 14 / 17.0Missense obs/exp: 164 / 175.4Syn Z: 0.92

ClinVar Variant Classifications

165 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic11
Likely Pathogenic5
VUS97
Likely Benign41
Benign4
Conflicting1
11
Pathogenic
5
Likely Pathogenic
97
VUS
41
Likely Benign
4
Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
2
2
7
0
11
Likely Pathogenic
1
0
4
0
5
VUS
7
77
13
0
97
Likely Benign
0
5
11
25
41
Benign
0
1
1
2
4
Conflicting
—1
Total10853627159

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

View in ClinVar →

Protein Context — Lollipop Plot

NSUN3 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients