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TRMT10A tRNA methyltransferase 10A [ Homo sapiens (human) ]

Gene ID: 93587, updated on 23-Nov-2023

Summary

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Official Symbol
TRMT10Aprovided by HGNC
Official Full Name
tRNA methyltransferase 10Aprovided by HGNC
Primary source
HGNC:HGNC:28403
See related
Ensembl:ENSG00000145331 MIM:616013; AllianceGenome:HGNC:28403
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
MSSGM; TRM10; MSSGM1; RG9MTD2; HEL-S-88
Summary
This gene encodes a protein that belongs to the tRNA (Guanine-1)-methyltransferase family. A similar gene in yeast modifies several different tRNA species. Mutations in this gene are associated with microcephaly, short stature, and impaired glucose metabolism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
Expression
Ubiquitous expression in testis (RPKM 4.1), thyroid (RPKM 2.7) and 25 other tissues See more
Orthologs
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Genomic context

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See TRMT10A in Genome Data Viewer
Location:
4q23
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (99546711..99564039, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (102861479..102878808, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (100467868..100485196, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ADH7 promoter Neighboring gene alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:100367692-100368891 Neighboring gene chromosome 4 open reading frame 17 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:100484300-100485499 Neighboring gene microsomal triglyceride transfer protein Neighboring gene chromosome 4 open reading frame 54

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. Coordination of mRNA and tRNA methylations by TRMT10A. Ontiveros RJ, et al. Proc Natl Acad Sci U S A, 2020 Apr 7. PMID 32213595, Free PMC Article
  2. Pancreatic β-cell tRNA hypomethylation and fragmentation link TRMT10A deficiency with diabetes. Cosentino C, et al. Nucleic Acids Res, 2018 Nov 2. PMID 30247717, Free PMC Article
  3. tRNA methyltransferase homologue gene TRMT10A mutation in young adult-onset diabetes with intellectual disability, microcephaly and epilepsy. Yew TW, et al. Diabet Med, 2016 Sep. PMID 26526202, Free PMC Article
  4. Homozygous deletion of TRMT10A as part of a contiguous gene deletion in a syndrome of failure to thrive, delayed puberty, intellectual disability and diabetes mellitus. Zung A, et al. Am J Med Genet A, 2015 Dec. PMID 26297882
  5. Distinct high resolution genome profiles of early onset and late onset colorectal cancer integrated with gene expression data identify candidate susceptibility loci. Berg M, et al. Mol Cancer, 2010 May 6. PMID 20459617, Free PMC Article

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Functional characterization of the human tRNA methyltransferases TRMT10A and TRMT10B.
    Title: Functional characterization of the human tRNA methyltransferases TRMT10A and TRMT10B.
  2. transcripts with increased m(6)A upon TRMT10A ablation contain an overrepresentation of m(1)G9-containing tRNAs codons read by tRNA(Gln(TTG)), tRNA(Arg(CCG)), and tRNA(Thr(CGT)) These findings collectively reveal the presence of coordinated mRNA and tRNA methylations and demonstrate a mechanism for regulating gene expression through the interactions between mRNA and tRNA modifying enzymes.
    Title: Coordination of mRNA and tRNA methylations by TRMT10A.
  3. demonstrate that human TRMT10A (hTRMT10A) and human TRMT10B (hTRMT10B) are not biochemically redundant
    Title: Distinct substrate specificities of the human tRNA methyltransferases TRMT10A and TRMT10B.
  4. tRNA guanosine 9 hypomethylation leads to tRNAGln fragmentation and that 5'-tRNAGln fragments mediate TRMT10A deficiency-induced beta-cell death. This study unmasks tRNA hypomethylation and fragmentation as a hitherto unknown mechanism of pancreatic beta-cell demise relevant to monogenic and polygenic forms of diabetes.
    Title: Pancreatic β-cell tRNA hypomethylation and fragmentation link TRMT10A deficiency with diabetes.
  5. A homozygous G to T transition in exon 2 of gene TRMT10A at nucleotide position 79 of the coding sequence was identified in a family with young-adult onset diabetes with intellectual disability, microcephaly and epilepsy.
    Title: tRNA methyltransferase homologue gene TRMT10A mutation in young adult-onset diabetes with intellectual disability, microcephaly and epilepsy.
  6. Homozygous deletion of TRMT10A is associated with a syndrome of failure to thrive, delayed puberty, intellectual disability and diabetes mellitus.
    Title: Homozygous deletion of TRMT10A as part of a contiguous gene deletion in a syndrome of failure to thrive, delayed puberty, intellectual disability and diabetes mellitus.
  7. TRMT10A dysfunction is associated with abnormalities in glucose homeostasis, short stature and microcephaly.
    Title: TRMT10A dysfunction is associated with abnormalities in glucose homeostasis, short stature and microcephaly.
  8. This is the first study describing the impact of TRMT10A deficiency in mammals, highlighting a role in the pathogenesis of microcephaly and early onset diabetes.
    Title: tRNA methyltransferase homolog gene TRMT10A mutation in young onset diabetes and primary microcephaly in humans.
Submit: New GeneRIF Correction

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
Microcephaly, short stature, and impaired glucose metabolism 1
MedGen: C4014997 OMIM: 616033 GeneReviews: Not available
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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

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

  • FLJ20325, MGC27034

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables tRNA (guanosine(9)-N1)-methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables tRNA (guanosine(9)-N1)-methyltransferase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables tRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables tRNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in tRNA N1-guanine methylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in tRNA N1-guanine methylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in tRNA methylation IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in actin cytoskeleton IDA
Inferred from Direct Assay
more info
  
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular exosome HDA PubMed 
located_in nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
tRNA methyltransferase 10 homolog A
Names
RNA (guanine-9-)-methyltransferase domain-containing protein 2
epididymis secretory protein Li 88
tRNA (guanine(9)-N(1))-methyltransferase TRMT10A
NP_001128137.1
NP_001128138.1
NP_001362809.1
NP_001362810.1
NP_001362811.1
NP_689505.1
XP_047272374.1
XP_054207242.1

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_041774.1 RefSeqGene

    Range
    5019..22347
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001134665.3 → NP_001128137.1  tRNA methyltransferase 10 homolog A isoform 1

    See identical proteins and their annotated locations for NP_001128137.1

    Status: REVIEWED

    Source sequence(s)
    AC083902, AK313548, AW242551, BC028373, DB455183
    Consensus CDS
    CCDS3650.1
    UniProtKB/Swiss-Prot
    B2R8X7, Q8TBZ6, Q9Y2T9
    UniProtKB/TrEMBL
    A0A024RDJ9, V9HVY8
    Related
    ENSP00000378342.2, ENST00000394876.7
    Conserved Domains (1) summary
    cd18101
    Location:101 → 276
    Trm10euk_A; eukaryotic tRNA m1G9 methyltransferase Trm10 homolog A

  2. NM_001134666.3 → NP_001128138.1  tRNA methyltransferase 10 homolog A isoform 1

    See identical proteins and their annotated locations for NP_001128138.1

    Status: REVIEWED

    Source sequence(s)
    AC083902, AK000332, AW242551, BC028373, DB455183
    Consensus CDS
    CCDS3650.1
    UniProtKB/Swiss-Prot
    B2R8X7, Q8TBZ6, Q9Y2T9
    UniProtKB/TrEMBL
    A0A024RDJ9, V9HVY8
    Related
    ENSP00000378343.3, ENST00000394877.7
    Conserved Domains (1) summary
    cd18101
    Location:101 → 276
    Trm10euk_A; eukaryotic tRNA m1G9 methyltransferase Trm10 homolog A

  3. NM_001375880.1 → NP_001362809.1  tRNA methyltransferase 10 homolog A isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC083902
    Consensus CDS
    CCDS3650.1
    UniProtKB/Swiss-Prot
    B2R8X7, Q8TBZ6, Q9Y2T9
    UniProtKB/TrEMBL
    A0A024RDJ9, V9HVY8
    Conserved Domains (1) summary
    cd18101
    Location:101 → 276
    Trm10euk_A; eukaryotic tRNA m1G9 methyltransferase Trm10 homolog A

  4. NM_001375881.1 → NP_001362810.1  tRNA methyltransferase 10 homolog A isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC083902
    Consensus CDS
    CCDS3650.1
    UniProtKB/Swiss-Prot
    B2R8X7, Q8TBZ6, Q9Y2T9
    UniProtKB/TrEMBL
    A0A024RDJ9, V9HVY8
    Conserved Domains (1) summary
    cd18101
    Location:101 → 276
    Trm10euk_A; eukaryotic tRNA m1G9 methyltransferase Trm10 homolog A

  5. NM_001375882.1 → NP_001362811.1  tRNA methyltransferase 10 homolog A isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC083902
    Conserved Domains (1) summary
    cd18101
    Location:101 → 269
    Trm10euk_A; eukaryotic tRNA m1G9 methyltransferase Trm10 homolog A

  6. NM_152292.5 → NP_689505.1  tRNA methyltransferase 10 homolog A isoform 1

    See identical proteins and their annotated locations for NP_689505.1

    Status: REVIEWED

    Source sequence(s)
    AC083902, AW242551, BC028373
    Consensus CDS
    CCDS3650.1
    UniProtKB/Swiss-Prot
    B2R8X7, Q8TBZ6, Q9Y2T9
    UniProtKB/TrEMBL
    A0A024RDJ9, V9HVY8
    Related
    ENSP00000273962.3, ENST00000273962.7
    Conserved Domains (1) summary
    cd18101
    Location:101 → 276
    Trm10euk_A; eukaryotic tRNA m1G9 methyltransferase Trm10 homolog A

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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    99546711..99564039 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047416418.1 → XP_047272374.1  tRNA methyltransferase 10 homolog A isoform X1

    UniProtKB/Swiss-Prot
    B2R8X7, Q8TBZ6, Q9Y2T9
    UniProtKB/TrEMBL
    A0A024RDJ9, V9HVY8

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    102861479..102878808 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054351267.1 → XP_054207242.1  tRNA methyltransferase 10 homolog A isoform X1

    UniProtKB/Swiss-Prot
    B2R8X7, Q8TBZ6, Q9Y2T9
    UniProtKB/TrEMBL
    A0A024RDJ9, V9HVY8
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TBZ6.1 GenPept UniProtKB/Swiss-Prot:Q8TBZ6

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