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

Gene ID: 54888, updated on 11-Apr-2024

Summary

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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
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Genomic context

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Location:
5p15.31
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (6599239..6633044, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (6529664..6563719, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (6599352..6633157, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374639 Neighboring gene ubiquitin conjugating enzyme E2 QL1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22331 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22333 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15897 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22334 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:6583428-6583589 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15898 Neighboring gene long intergenic non-protein coding RNA 1018 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:6633253-6633764 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:6633765-6634276 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:6648951-6649644 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:6649645-6650336 Neighboring gene steroid 5 alpha-reductase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22335 Neighboring gene uncharacterized LOC124900934

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. The RNA m5C Methylase NSUN2 Modulates Corneal Epithelial Wound Healing. Luo G, et al. Invest Ophthalmol Vis Sci, 2023 Mar 1. PMID 36862118, Free PMC Article
  2. NSUN2 gene rs13181449 C>T polymorphism reduces neuroblastoma risk. Lin L, et al. Gene, 2023 Feb 20. PMID 36529349
  3. Reorganization of the Landscape of Translated mRNAs in NSUN2-Deficient Cells and Specific Features of NSUN2 Target mRNAs. Kossinova OA, et al. Int J Mol Sci, 2022 Aug 28. PMID 36077143, Free PMC Article
  4. NSun2 promotes cell migration through methylating autotaxin mRNA. Xu X, et al. J Biol Chem, 2020 Dec 25. PMID 33093178, Free PMC Article
  5. Expanding the phenotype of biallelic loss-of-function variants in the NSUN2 gene: Description of four individuals with juvenile cataract, chronic nephritis, or brain anomaly as novel complications. Kato K, et al. Am J Med Genet A, 2021 Jan. PMID 33084202

See all (177) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. NSUN2-mediated m5C modification of HBV RNA positively regulates HBV replication.
    Title: NSUN2-mediated m5C modification of HBV RNA positively regulates HBV replication.
  4. 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.
  5. 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.
  6. Aberrant m5C hypermethylation mediates intrinsic resistance to gefitinib through NSUN2/YBX1/QSOX1 axis in EGFR-mutant non-small-cell lung cancer.
    Title: Aberrant m5C hypermethylation mediates intrinsic resistance to gefitinib through NSUN2/YBX1/QSOX1 axis in EGFR-mutant non-small-cell lung cancer.
  7. The RNA m5C Methylase NSUN2 Modulates Corneal Epithelial Wound Healing.
    Title: The RNA m5C Methylase NSUN2 Modulates Corneal Epithelial Wound Healing.
  8. NSUN2 promotes osteosarcoma progression by enhancing the stability of FABP5 mRNA via m[5]C methylation.
    Title: NSUN2 promotes osteosarcoma progression by enhancing the stability of FABP5 mRNA via m(5)C methylation.
  9. m[5]C-dependent cross-regulation between nuclear reader ALYREF and writer NSUN2 promotes urothelial bladder cancer malignancy through facilitating RABL6/TK1 mRNAs splicing and stabilization.
    Title: m(5)C-dependent cross-regulation between nuclear reader ALYREF and writer NSUN2 promotes urothelial bladder cancer malignancy through facilitating RABL6/TK1 mRNAs splicing and stabilization.
  10. NSUN2 gene rs13181449 C>T polymorphism reduces neuroblastoma risk.
    Title: NSUN2 gene rs13181449 C>T polymorphism reduces neuroblastoma risk.
Submit: New GeneRIF Correction See all GeneRIFs (52)

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
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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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ20303

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables mRNA (cytidine-5-)-methyltransferase activity IDA
Inferred from Direct Assay
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 modification 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 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
NP_060225.4
XP_054208843.1

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.

Genomic

  1. NG_028215.1 RefSeqGene

    Range
    5317..39122
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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]

  2. 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

  1. 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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    6599239..6633044 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    6529664..6563719 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054352868.1 → XP_054208843.1  RNA cytosine C(5)-methyltransferase NSUN2 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q08J23.2 GenPept UniProtKB/Swiss-Prot:Q08J23

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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