NSUN2 NOP2/Sun RNA methyltransferase 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NSUN2provided by HGNC
Official Full Name: NOP2/Sun RNA methyltransferase 2provided by HGNC
Primary source: HGNC:HGNC:25994
See related: Ensembl:ENSG00000037474 MIM:610916; AllianceGenome:HGNC:25994
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: MISU; MRT5; SAKI; TRM4
Summary: This gene encodes a methyltransferase that catalyzes the methylation of cytosine to 5-methylcytosine (m5C) at position 34 of intron-containing tRNA(Leu)(CAA) precursors. This modification is necessary to stabilize the anticodon-codon pairing and correctly translate the mRNA. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene.[provided by RefSeq, Mar 2011]
Expression: Ubiquitous expression in lymph node (RPKM 14.3), appendix (RPKM 14.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5p15.31

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (6599239..6633044, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (6529664..6563719, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (6599352..6633157, complement)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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?

NSUN2/YBX1 promotes the progression of breast cancer by enhancing HGH1 mRNA stability through m[5]C methylation.
Title: NSUN2/YBX1 promotes the progression of breast cancer by enhancing HGH1 mRNA stability through m(5)C methylation.
NSUN2 affects diabetic retinopathy progression by regulating MUC1 expression through RNA m[5]C methylation.
Title: NSUN2 affects diabetic retinopathy progression by regulating MUC1 expression through RNA m(5)C methylation.
5-Methylcytosine transferase NSUN2 drives NRF2-mediated ferroptosis resistance in non-small cell lung cancer.
Title: 5-Methylcytosine transferase NSUN2 drives NRF2-mediated ferroptosis resistance in non-small cell lung cancer.
NSUN2 promotes lung adenocarcinoma progression through stabilizing PIK3R2 mRNA in an m[5]C-dependent manner.
Title: NSUN2 promotes lung adenocarcinoma progression through stabilizing PIK3R2 mRNA in an m(5)C-dependent manner.
NSUN2-Mediated m[5]C Methylation Impairs Endometrial Receptivity.
Title: NSUN2-Mediated m(5)C Methylation Impairs Endometrial Receptivity.
LncRNA HOST2 promotes NSUN2-mediated breast cancer progression via interaction with ELAVL1.
Title: LncRNA HOST2 promotes NSUN2-mediated breast cancer progression via interaction with ELAVL1.
NSUN2-mediated mRNA m[5]C Modification Regulates the Progression of Hepatocellular Carcinoma.
Title: NSUN2-mediated mRNA m(5)C Modification Regulates the Progression of Hepatocellular Carcinoma.
NSUN2-mediated m5C modification of HBV RNA positively regulates HBV replication.
Title: NSUN2-mediated m5C modification of HBV RNA positively regulates HBV replication.
NSUN2 is a glucose sensor suppressing cGAS/STING to maintain tumorigenesis and immunotherapy resistance.
Title: NSUN2 is a glucose sensor suppressing cGAS/STING to maintain tumorigenesis and immunotherapy resistance.
NSUN2-mediated m[5] C RNA methylation dictates retinoblastoma progression through promoting PFAS mRNA stability and expression.
Title: NSUN2-mediated m(5) C RNA methylation dictates retinoblastoma progression through promoting PFAS mRNA stability and expression.

Submit: New GeneRIF Correction See all GeneRIFs (57)

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
Intellectual disability, autosomal recessive 5 MedGen: C1970199 OMIM: 611091 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. 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)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Pr55(Gag)	gag	Interaction of HIV-1 Gag with NOP2/Sun RNA methyltransferase family, member 2 (NSUN2) is identified in a series of six affinity purification/mass spectrometry screens	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH92904 (e-PCR)
- UniSTS:83796

D5S2678 (e-PCR)
- UniSTS:55956

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables mRNA (cytidine-5-)-methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables tRNA (cytidine-5-)-methyltransferase activity	EXP Inferred from Experiment more info	PubMed
enables tRNA (cytidine-5-)-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	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in hair follicle maturation	ISS Inferred from Sequence or Structural Similarity more info
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
involved_in mRNA processing	IDA Inferred from Direct Assay more info	PubMed
involved_in meiotic cell cycle checkpoint signaling	IEA Inferred from Electronic Annotation more info
involved_in regulation of mRNA export from nucleus	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of stem cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in spermatid development	IEA Inferred from Electronic Annotation more info
involved_in tRNA methylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in tRNA methylation	IDA Inferred from Direct Assay more info	PubMed
involved_in tRNA modification	TAS Traceable Author Statement more info
involved_in tRNA stabilization	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in chromatoid body	IEA Inferred from Electronic Annotation more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	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
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in spindle	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: RNA cytosine C(5)-methyltransferase NSUN2

Names: 5-methycytoisine methyltransferase; Myc-induced SUN-domain-containing protein; NOL1/NOP2/Sun domain family, member 2; NOP2/Sun RNA methyltransferase family member 2; NOP2/Sun domain family, member 2; mRNA cytosine C(5)-methyltransferase; myc-induced SUN domain-containing protein; substrate of AIM1/Aurora kinase B; tRNA (cytosine(34)-C(5))-methyltransferase; tRNA (cytosine-5-)-methyltransferase NSUN2; tRNA cytosine C(5)-methyltransferase; tRNA methyltransferase 4 homolog

NP_001180384.1

EC 2.1.1.203

NP_060225.4

EC 2.1.1.203

XP_054208843.1

EC 2.1.1.203

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.

Genomic

NG_028215.1 RefSeqGene

Range

5317..39122

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001193455.2 → NP_001180384.1 RNA cytosine C(5)-methyltransferase NSUN2 isoform 2

See identical proteins and their annotated locations for NP_001180384.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an in-frame coding exon in the 5' region compared to variant 1. This results in a shorter isoform (2) missing an internal protein segment compared to isoform 1.

Source sequence(s)

AK298980, BC001041, BF000644, BG387061

Consensus CDS

CCDS54832.1

UniProtKB/Swiss-Prot

Q08J23

Related

ENSP00000420957.1, ENST00000506139.5

Conserved Domains (1) summary

COG0144
Location:28 → 396

RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]
NM_017755.6 → NP_060225.4 RNA cytosine C(5)-methyltransferase NSUN2 isoform 1

See identical proteins and their annotated locations for NP_060225.4

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the predominant transcript and encodes the longer isoform (1).

Source sequence(s)

AB255451, BC001041, BF000644

Consensus CDS

CCDS3869.1

UniProtKB/Swiss-Prot

A8K529, B2RNR4, B3KP09, B4DQW2, G3V1R4, Q08J23, Q9BVN4, Q9H858, Q9NXD9

Related

ENSP00000264670.6, ENST00000264670.11

Conserved Domains (1) summary

COG0144
Location:28 → 431

RsmB; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]

RNA

NR_037947.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an internal exon compared to variant 1. This causes a frame-shift and premature translation termination, rendering this transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AB255451, BC001041

Related

ENST00000504374.5