NSUN3 NOP2/Sun RNA methyltransferase 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NSUN3provided by HGNC
Official Full Name: NOP2/Sun RNA methyltransferase 3provided by HGNC
Primary source: HGNC:HGNC:26208
See related: Ensembl:ENSG00000178694 MIM:617491; AllianceGenome:HGNC:26208
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: MST077; COXPD48; MSTP077
Summary: Enables tRNA (cytidine-5-)-methyltransferase activity. Involved in regulation of mitochondrial translation and tRNA wobble base cytosine methylation. Located in mitochondrial matrix. Implicated in combined oxidative phosphorylation deficiency 48. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in colon (RPKM 4.7), testis (RPKM 4.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q11.2

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (94063061..94131832)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (96761512..96830315)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (93781905..93850676)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RNA 5-Methylcytosine Regulator NSUN3 promotes tumor progression through regulating immune infiltration in head and neck squamous cell carcinoma.
Title: RNA 5-Methylcytosine Regulator NSUN3 promotes tumor progression through regulating immune infiltration in head and neck squamous cell carcinoma.
NSUN3-mediated mitochondrial tRNA 5-formylcytidine modification is essential for embryonic development and respiratory complexes in mice.
Title: NSUN3-mediated mitochondrial tRNA 5-formylcytidine modification is essential for embryonic development and respiratory complexes in mice.
Novel Biallelic NSUN3 Variants Cause Early-Onset Mitochondrial Encephalomyopathy and Seizures.
Title: Novel Biallelic NSUN3 Variants Cause Early-Onset Mitochondrial Encephalomyopathy and Seizures.
The authors show that the RNA methyltransferase NSUN3 localises to mitochondria and interacts with mt-tRNA(M)(et) to methylate cytosine 34 (C34) at the wobble position.
Title: NSUN3 and ABH1 modify the wobble position of mt-tRNAMet to expand codon recognition in mitochondrial translation.
The NSUN3-knockout cells showed strong reduction in mitochondrial protein synthesis and reduced oxygen consumption, leading to deficient mitochondrial activity. It reconstituted formation of 5-methylcytidine (m(5)C) at position 34 (m(5)C34) on mt-tRNA(Met) with recombinant NSUN3 in the presence of AdoMet, demonstrating that NSUN3-mediated m(5)C34 formation initiates f(5)C34 biogenesis.
Title: NSUN3 methylase initiates 5-formylcytidine biogenesis in human mitochondrial tRNA(Met).
Observational study of gene-disease association. (HuGE Navigator)
Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Combined oxidative phosphorylation deficiency 48 MedGen: C5436602 OMIM: 619012 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genome-wide association study identifies 8 novel loci associated with blood pressure responses to interventions in Han Chinese. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-33570 (e-PCR)
- UniSTS:82704

SHGC-142686 (e-PCR)
- UniSTS:171592

SHGC-36500 (e-PCR)
- UniSTS:10323

RH35958 (e-PCR)
- UniSTS:85618

D1S1425 (e-PCR)
- UniSTS:149621

RH80683 (e-PCR)
- UniSTS:87161

RH41657 (e-PCR)
- UniSTS:90535

RH69243 (e-PCR)
- UniSTS:87012

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables tRNA (cytidine-5-)-methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables tRNA binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in rRNA methylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of mitochondrial translation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in tRNA wobble base cytosine methylation	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of mitochondrial large ribosomal subunit	IBA Inferred from Biological aspect of Ancestor more info
located_in mitochondrial matrix	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrion	HTP more info	PubMed
located_in mitochondrion	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: tRNA (cytosine(34)-C(5))-methyltransferase, mitochondrial

Names: NOL1/NOP2/Sun domain family member 3; NOP2/Sun RNA methyltransferase family member 3; putative methyltransferase NSUN3

NP_071355.1

EC 2.1.1.-

XP_047304640.1

EC 2.1.1.-

XP_054203464.1

EC 2.1.1.-

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_022072.5 → NP_071355.1 tRNA (cytosine(34)-C(5))-methyltransferase, mitochondrial

See identical proteins and their annotated locations for NP_071355.1

Status: VALIDATED

Source sequence(s)

AC019233, BC020602, BQ030336

Consensus CDS

CCDS2927.1

UniProtKB/Swiss-Prot

Q6PG41, Q8IXG9, Q9H649, Q9H6M2

Related

ENSP00000318986.4, ENST00000314622.9

Conserved Domains (1) summary

cl17173
Location:124 → 332

AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...