NSUN4

Chr 1

NOP2/Sun RNA methyltransferase 4

Also known as: SHTAP

NCBI Gene: 387338ENSG00000117481UniProt: Q96CB9OMIM: 615394

The protein is a mitochondrial RNA cytosine methyltransferase that modifies mitochondrial ribosomal RNAs and messenger RNAs, playing a critical role in mitochondrial ribosome biogenesis and function. Mutations cause autosomal recessive combined oxidative phosphorylation deficiency-37, a severe mitochondrial disorder affecting energy metabolism. The gene is extremely intolerant to loss-of-function variants, indicating that complete protein loss is likely incompatible with normal cellular function.

OMIMResearchSummary from RefSeq, UniProt
DNmechanismLOEUF 0.91
Clinical Summary— NSUN4
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
6 unique Pathogenic / Likely Pathogenic· 54 VUS of 78 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
0.91LOEUF
pLI 0.000
Z-score 1.87
OE 0.57 (0.37–0.91)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
0.83Z-score
OE missense 0.84 (0.74–0.95)
183 obs / 217.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.57 (0.37–0.91)
0≤0.351.4
Missense OE0.84 (0.74–0.95)
0≤0.61.4
Synonymous OE0.86
0≤1.21.6
LoF obs/exp: 13 / 22.6Missense obs/exp: 183 / 217.5Syn Z: 1.03
DN
0.6258th %ile
GOF
0.4579th %ile
LOF
0.2969th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

78 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic4
Likely Pathogenic2
VUS54
4
Pathogenic
2
Likely Pathogenic
54
VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
4
0
4
Likely Pathogenic
0
0
2
0
2
VUS
0
48
6
0
54
Likely Benign
0
0
0
0
0
Benign
0
0
0
0
0
Total04812060

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

View in ClinVar →

Protein Context — Lollipop Plot

NSUN4 · 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