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

Gene ID: 93587, updated on 6-Nov-2019

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
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
mouse all

Genomic context

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See TRMT10A in Genome Data Viewer
Location:
4q23
Exon count:
9
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (99546709..99564039, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (100467864..100485189, 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 chromosome 4 open reading frame 17 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. 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
  2. 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
  3. 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
  4. 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
  5. TRMT10A dysfunction is associated with abnormalities in glucose homeostasis, short stature and microcephaly. Gillis D, et al. J Med Genet, 2014 Sep. PMID 25053765

See all (14) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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 BioSystems

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  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • tRNA modification in the nucleus and cytosol, organism-specific biosystem (from REACTOME)
    tRNA modification in the nucleus and cytosol, organism-specific biosystemAt least 92 distinct tRNA nucleotide base modifications have been found. The modifications are made post-transcriptionally by a large group of disparate enzymes located in the nucleus, cytosol, and m...
  • tRNA processing, organism-specific biosystem (from REACTOME)
    tRNA processing, organism-specific biosystemGenes encoding transfer RNAs (tRNAs) are transcribed by RNA polymerase III in the nucleus and by mitochondrial RNA polymerase in the mitochondrion.In the nucleus transcription reactions produce precu...

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
RNA binding HDA PubMed 
tRNA (guanine(9)-N(1))-methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
tRNA (guanine-N1-)-methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
tRNA (guanine-N1-)-methyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
tRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
tRNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
mitochondrial tRNA processing IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
tRNA methylation IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
actin cytoskeleton IDA
Inferred from Direct Assay
more info
  
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
extracellular exosome HDA PubMed 
mitochondrion IEA
Inferred from Electronic Annotation
more info
  
nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 
nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
  
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
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_689505.1
XP_005263409.1
XP_006714480.1

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
    Q8TBZ6
    UniProtKB/TrEMBL
    V9HVY8
    Related
    ENSP00000378342.2, ENST00000394876.7
    Conserved Domains (1) summary
    cl00407
    Location:112 → 276
    tRNA_m1G_MT; tRNA (Guanine-1)-methyltransferase

  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
    Q8TBZ6
    UniProtKB/TrEMBL
    V9HVY8
    Related
    ENSP00000378343.3, ENST00000394877.7
    Conserved Domains (1) summary
    cl00407
    Location:112 → 276
    tRNA_m1G_MT; tRNA (Guanine-1)-methyltransferase

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

    Status: REVIEWED

    Source sequence(s)
    AC083902

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

    Status: REVIEWED

    Source sequence(s)
    AC083902

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

    Status: REVIEWED

    Source sequence(s)
    AC083902

  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
    Q8TBZ6
    UniProtKB/TrEMBL
    V9HVY8
    Related
    ENSP00000273962.3, ENST00000273962.7
    Conserved Domains (1) summary
    cl00407
    Location:112 → 276
    tRNA_m1G_MT; tRNA (Guanine-1)-methyltransferase

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    99546709..99564039 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006714417.2 → XP_006714480.1  tRNA methyltransferase 10 homolog A isoform X1

    UniProtKB/Swiss-Prot
    Q8TBZ6
    UniProtKB/TrEMBL
    V9HVY8
    Conserved Domains (1) summary
    cl00407
    Location:112 → 276
    tRNA_m1G_MT; tRNA (Guanine-1)-methyltransferase

  2. XM_005263352.3 → XP_005263409.1  tRNA methyltransferase 10 homolog A isoform X1

    UniProtKB/Swiss-Prot
    Q8TBZ6
    UniProtKB/TrEMBL
    V9HVY8
    Conserved Domains (1) summary
    cl00407
    Location:112 → 276
    tRNA_m1G_MT; tRNA (Guanine-1)-methyltransferase
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TBZ6.1 GenPept UniProtKB/Swiss-Prot:Q8TBZ6

Gene LinkOut

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

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