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

    Gene ID: 93587, updated on 10-Dec-2024

    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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (99546711..99564039, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (102861479..102878808, complement)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. 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
    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. 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
    4. 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
    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 (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TRMT10A dysfunction perturbs codon translation of initiator methionine and glutamine and impairs brain functions in mice.
      Title: TRMT10A dysfunction perturbs codon translation of initiator methionine and glutamine and impairs brain functions in mice.
    2. Functional characterization of the human tRNA methyltransferases TRMT10A and TRMT10B.
      Title: Functional characterization of the human tRNA methyltransferases TRMT10A and TRMT10B.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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_2024_08

    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

    Gene LinkOut

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

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