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10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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NSUN3
NOP2/Sun RNA methyltransferase 3
Chromosome 3 Β· 3q11.2
NCBI Gene: 63899Ensembl: ENSG00000178694.10HGNC: HGNC:26208UniProt: Q9H649
20PubMed Papers
21Diseases
0Drugs
5Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
regulation of mitochondrial translationmitochondrionmitochondrial matrixtRNA wobble base cytosine methylationcombined oxidative phosphorylation deficiency 48genetic disorderclear cell renal carcinomadeep vein thrombosis
✦AI Summary

NSUN3 is a mitochondrial tRNA methyltransferase that catalyzes 5-methylcytosine (m5C) formation at position 34 of mitochondrial tRNA(Met), initiating subsequent 5-formylcytosine (f5C) modification at the wobble position 123. This modification enables recognition of both AUG and AUA codons, expanding mitochondrial translation capacity 23. Mechanistically, NSUN3-mediated m5C modification stabilizes target mRNAs through enhanced mRNA stability. Beyond tRNA substrates, NSUN3 regulates expression of mitochondrial oxidative phosphorylation complex subunits and non-coding RNAs 45. Recent studies demonstrate NSUN3 modulates inflammatory responses in sepsis by stabilizing TAK1 and TIFA mRNAs through m5C modification 67. Disease relevance is substantial: biallelic NSUN3 mutations cause combined oxidative phosphorylation deficiency 48 with phenotypic heterogeneity ranging from isolated optic atrophy to severe early-onset multisystem mitochondrial disease 8. Tissue-specific NSUN3 loss impairs respiratory complex function and causes age-associated cardiac pathology 9. Additionally, NSUN3 dysregulation correlates with sepsis severity and serves as a diagnostic biomarker 10. Cancer cells exploit NSUN3-dependent mitochondrial modifications to enhance metabolic plasticity for metastatic dissemination 4, suggesting therapeutic potential for targeting this pathway.

Sources cited
1
NSUN3 mediates m5C methylation at position 34 of mt-tRNA(Met)
PMID: 27214402
2
NSUN3-catalyzed m5C modification at wobble position enables AUA codon recognition
PMID: 27356879
3
NSUN3 methylation at cytosine 34 initiates f5C formation for AUA codon translation
PMID: 27497299
4
NSUN3-dependent m5C modifications drive metastatic cancer cell metabolic plasticity
PMID: 35768510
5
NSUN3 is upregulated in sepsis cluster with mRNA stability regulation functions
PMID: 37701433
6
NSUN3 m5C methylation regulates variant gene expression in Plasmodium falciparum
PMID: 40148982
7
NSUN3-mediated m5C modification stabilizes TAK1 mRNA in sepsis-induced pulmonary injury
PMID: 40482605
8
NSUN3 stabilizes TIFA mRNA through m5C modification in sepsis-associated acute kidney injury
PMID: 39924309
9
NSUN3 is essential for embryonic development and respiratory complex function in mice
PMID: 36949224
10
Biallelic NSUN3 variants cause diverse phenotypes from optic atrophy to severe mitochondrial disorder
PMID: 40465263
Disease Associationsβ“˜21
combined oxidative phosphorylation deficiency 48Open Targets
0.71Strong
genetic disorderOpen Targets
0.41Moderate
clear cell renal carcinomaOpen Targets
0.37Weak
deep vein thrombosisOpen Targets
0.33Weak
renal carcinomaOpen Targets
0.30Weak
ThromboembolismOpen Targets
0.30Weak
venous thromboembolismOpen Targets
0.26Weak
type 2 diabetes mellitusOpen Targets
0.20Weak
diabetes mellitusOpen Targets
0.17Weak
heart diseaseOpen Targets
0.17Weak
smoking initiationOpen Targets
0.16Weak
Pulmonary InfarctionOpen Targets
0.16Weak
Abnormality of the skeletal systemOpen Targets
0.16Weak
risk-taking behaviourOpen Targets
0.16Weak
esophageal cancerOpen Targets
0.16Weak
pulmonary embolismOpen Targets
0.15Weak
mathematical abilityOpen Targets
0.14Weak
obesityOpen Targets
0.13Weak
cutaneous lupus erythematosusOpen Targets
0.13Weak
synovium disorderOpen Targets
0.13Weak
Combined oxidative phosphorylation deficiency 48UniProt
Pathogenic Variants5
NM_022072.5(NSUN3):c.150G>A (p.Trp50Ter)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2022β†’ Residue 50
NM_022072.5(NSUN3):c.465dup (p.Gly156fs)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2018β†’ Residue 156
NM_022072.5(NSUN3):c.123-615_466+2155delPathogenic
Combined oxidative phosphorylation deficiency 48
β˜†β˜†β˜†β˜†2020
NM_022072.5(NSUN3):c.454T>A (p.Cys152Ser)Pathogenic
Combined oxidative phosphorylation deficiency 48
β˜†β˜†β˜†β˜†2020β†’ Residue 152
NM_022072.5(NSUN3):c.421G>C (p.Ala141Pro)Pathogenic
Combined oxidative phosphorylation deficiency 48
β˜†β˜†β˜†β˜†2020β†’ Residue 141
View on ClinVar β†—
Related Genes
BRIX1Protein interaction100%TRDMT1Protein interaction93%HNRNPKProtein interaction89%NSUN5Protein interaction79%MTFMTProtein interaction79%ALYREFProtein interaction72%
Tissue Expression6 tissues
Bone Marrow
100%
Heart
61%
Brain
47%
Liver
43%
Ovary
42%
Lung
40%
Gene Interaction Network
Click a node to explore
NSUN3BRIX1TRDMT1HNRNPKNSUN5MTFMTALYREF
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt Q9H649
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.80LoF Tolerant
pLIβ“˜
0.01Tolerant
Observed/Expected LoF0.52 [0.35–0.80]
RankingsWhere NSUN3 stands among ~20K protein-coding genes
  • #14,210of 20,598
    Most Researched20
  • #3,637of 5,498
    Most Pathogenic Variants5
  • #6,585of 17,882
    Most Constrained (LOEUF)0.80
Genes detectedNSUN3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Mitochondrial RNA modifications shape metabolic plasticity in metastasis.
PMID: 35768510
Nature Β· 2022
1.00
2
Identification and validation of key biomarkers based on RNA methylation genes in sepsis.
PMID: 37701433
Front Immunol Β· 2023
0.90
3
m5C methylation of mitochondrial RNA and non-coding RNA by NSUN3 is associated with variant gene expression and asexual blood-stage development in Plasmodium falciparum.
PMID: 40148982
Parasit Vectors Β· 2025
0.80
4
RNA cytosine methylation and methyltransferases mediate chromatin organization and 5-azacytidine response and resistance in leukaemia.
PMID: 29563491
Nat Commun Β· 2018
0.70
5
NSUN3-mediated m
PMID: 40482605
Mol Immunol Β· 2025
0.60