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    TRMT1 tRNA methyltransferase 1 [ Homo sapiens (human) ]

    Gene ID: 55621, updated on 27-Nov-2024

    Summary

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    Official Symbol
    TRMT1provided by HGNC
    Official Full Name
    tRNA methyltransferase 1provided by HGNC
    Primary source
    HGNC:HGNC:25980
    See related
    Ensembl:ENSG00000104907 MIM:611669; AllianceGenome:HGNC:25980
    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
    TRM1; MRT68
    Summary
    This gene encodes a tRNA-modifying enzyme that acts as a dimethyltransferase, modifying a single guanine residue at position 26 of the tRNA. The encoded enzyme has both mono- and dimethylase activity when exogenously expressed, and uses S-adenosyl methionine as a methyl donor. The C-terminal region of the encoded protein has both a zinc finger motif, and an arginine/proline-rich region. Mutations in this gene have been implicated in autosomal recessive intellectual disorder (ARID). Alternative splicing results in multiple transcript variants encoding different isoforms. There is a pseudogene of this gene on the X chromosome. [provided by RefSeq, May 2017]
    Expression
    Ubiquitous expression in spleen (RPKM 12.4), lymph node (RPKM 11.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TRMT1 in Genome Data Viewer
    Location:
    19p13.13
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (13104907..13116740, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (13230119..13241953, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (13215721..13227554, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13210189-13211052 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14106 Neighboring gene CRISPRi-FlowFISH-validated CALR, DNASE2 and KLF1 regulatory element Neighboring gene Sharpr-MPRA regulatory region 14065 Neighboring gene uncharacterized LOC105372282 Neighboring gene LYL1 basic helix-loop-helix family member Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10191 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13220465-13220965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14110 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10192 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10193 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13230123-13230624 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13230625-13231125 Neighboring gene nucleus accumbens associated 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10194 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14111 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13234142-13234801 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13247773-13248692 Neighboring gene syntaxin 10 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10195 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10196 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14112

    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. TRMT1-Catalyzed tRNA Modifications Are Required for Redox Homeostasis To Ensure Proper Cellular Proliferation and Oxidative Stress Survival. Dewe JM, et al. Mol Cell Biol, 2017 Nov 1. PMID 28784718, Free PMC Article
    2. Mutations in the tRNA methyltransferase 1 gene TRMT1 cause congenital microcephaly, isolated inferior vermian hypoplasia and cystic leukomalacia in addition to intellectual disability. Blaesius K, et al. Am J Med Genet A, 2018 Nov. PMID 30289604
    3. Human TRMT1 catalyzes m(2)G or m(2)(2)G formation on tRNAs in a substrate-dependent manner. Xiong QP, et al. Sci China Life Sci, 2023 Oct. PMID 37204604
    4. SARS-CoV-2 main protease Nsp5 cleaves and inactivates human tRNA methyltransferase TRMT1. Lu JL, et al. J Mol Cell Biol, 2023 Aug 3. PMID 37073102, Free PMC Article
    5. An intellectual disability-associated missense variant in TRMT1 impairs tRNA modification and reconstitution of enzymatic activity. Zhang K, et al. Hum Mutat, 2020 Mar. PMID 31898845, Free PMC Article

    See all (63) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Proteolytic cleavage and inactivation of the TRMT1 tRNA modification enzyme by SARS-CoV-2 main protease.
      Title: Proteolytic cleavage and inactivation of the TRMT1 tRNA modification enzyme by SARS-CoV-2 main protease.
    2. Human TRMT1 catalyzes m[2]G or m[2]2G formation on tRNAs in a substrate-dependent manner.
      Title: Human TRMT1 catalyzes m(2)G or m(2)(2)G formation on tRNAs in a substrate-dependent manner.
    3. SARS-CoV-2 main protease Nsp5 cleaves and inactivates human tRNA methyltransferase TRMT1.
      Title: SARS-CoV-2 main protease Nsp5 cleaves and inactivates human tRNA methyltransferase TRMT1.
    4. An intellectual disability-associated missense variant in TRMT1 impairs tRNA modification and reconstitution of enzymatic activity.
      Title: An intellectual disability-associated missense variant in TRMT1 impairs tRNA modification and reconstitution of enzymatic activity.
    5. mutations in the methyltransferase TRMT1 lead to a microcephalic phenotype and isolated inferior vermian hypoplasia
      Title: Mutations in the tRNA methyltransferase 1 gene TRMT1 cause congenital microcephaly, isolated inferior vermian hypoplasia and cystic leukomalacia in addition to intellectual disability.
    6. Results uncover a biological role for TRMT1-catalyzed tRNA modification in redox metabolism and show that individuals with TRMT1-associated ID are likely to have major perturbations in cellular homeostasis due to the lack of m2,2G modifications.
      Title: TRMT1-Catalyzed tRNA Modifications Are Required for Redox Homeostasis To Ensure Proper Cellular Proliferation and Oxidative Stress Survival.
    7. a missense variant was found in GRM1 gene, while in the second family, a frameshift alteration was identified in TRMT1, both of which were found to co-segregate with the intellectual disability.
      Title: The Role of a Novel TRMT1 Gene Mutation and Rare GRM1 Gene Defect in Intellectual Disability in Two Azeri Families.
    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
    Intellectual developmental disorder, autosomal recessive 68
    MedGen: C4749033 OMIM: 618302 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

    • FLJ20244

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables tRNA (guanine(26)-N2)-dimethyltransferase activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables tRNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in tRNA N2-guanine methylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in tRNA modification TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    located_in mitochondrion HTP PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    tRNA (guanine(26)-N(2))-dimethyltransferase
    Names
    N(2),N(2)-dimethylguanosine tRNA methyltransferase
    TRM1 tRNA methyltransferase 1 homolog
    tRNA 2,2-dimethylguanosine-26 methyltransferase
    tRNA methyltransferase 1 homolog
    tRNA(guanine-26,N(2)-N(2)) methyltransferase
    tRNA(m(2,2)G26)dimethyltransferase
    NP_001129507.1
    NP_001136026.1
    NP_001338689.1
    NP_001338690.1
    NP_001338691.1
    NP_060192.1

    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_054900.1 RefSeqGene

      Range
      5828..17661
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001136035.4 → NP_001129507.1  tRNA (guanine(26)-N(2))-dimethyltransferase isoform 1

      See identical proteins and their annotated locations for NP_001129507.1

      Status: REVIEWED

      Source sequence(s)
      AC005546
      Consensus CDS
      CCDS12293.1
      UniProtKB/Swiss-Prot
      O76103, Q548Y5, Q8WVA6, Q9NXH9
      UniProtKB/TrEMBL
      A8K8L2
      Related
      ENSP00000350352.4, ENST00000357720.9
      Conserved Domains (3) summary
      smart00356
      Location:600 → 626
      ZnF_C3H1; zinc finger
      pfam02005
      Location:45 → 500
      TRM; N2,N2-dimethylguanosine tRNA methyltransferase
      cl25637
      Location:571 → 624
      DFRP_C; DRG Family Regulatory Proteins, Tma46

    2. NM_001142554.3 → NP_001136026.1  tRNA (guanine(26)-N(2))-dimethyltransferase isoform 2

      See identical proteins and their annotated locations for NP_001136026.1

      Status: REVIEWED

      Source sequence(s)
      AC005546, BC018302, DC313999
      Consensus CDS
      CCDS45997.1
      UniProtKB/TrEMBL
      A8K8L2
      Related
      ENSP00000221504.7, ENST00000221504.12
      Conserved Domains (3) summary
      smart00356
      Location:571 → 597
      ZnF_C3H1; zinc finger
      pfam02005
      Location:45 → 471
      TRM; N2,N2-dimethylguanosine tRNA methyltransferase
      cl25637
      Location:542 → 595
      DFRP_C; DRG Family Regulatory Proteins, Tma46

    3. NM_001351760.2 → NP_001338689.1  tRNA (guanine(26)-N(2))-dimethyltransferase isoform 2

      Status: REVIEWED

      Source sequence(s)
      AK000251, BQ212049, DC365548
      Consensus CDS
      CCDS45997.1
      UniProtKB/TrEMBL
      A8K8L2
      Conserved Domains (3) summary
      smart00356
      Location:571 → 597
      ZnF_C3H1; zinc finger
      pfam02005
      Location:45 → 471
      TRM; N2,N2-dimethylguanosine tRNA methyltransferase
      cl25637
      Location:542 → 595
      DFRP_C; DRG Family Regulatory Proteins, Tma46

    4. NM_001351761.2 → NP_001338690.1  tRNA (guanine(26)-N(2))-dimethyltransferase isoform 3

      Status: REVIEWED

      Source sequence(s)
      AK000251, DC373552
      UniProtKB/TrEMBL
      A8K8L2
      Related
      ENST00000593157.5
      Conserved Domains (3) summary
      smart00356
      Location:564 → 590
      ZnF_C3H1; zinc finger
      pfam02005
      Location:9 → 464
      TRM; N2,N2-dimethylguanosine tRNA methyltransferase
      cl25637
      Location:535 → 588
      DFRP_C; DRG Family Regulatory Proteins, Tma46

    5. NM_001351762.2 → NP_001338691.1  tRNA (guanine(26)-N(2))-dimethyltransferase isoform 4

      Status: REVIEWED

      Source sequence(s)
      AK000251, DA202329
      Related
      ENST00000588511.5
      Conserved Domains (3) summary
      smart00356
      Location:339 → 365
      ZnF_C3H1; zinc finger
      cl17173
      Location:1 → 239
      AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...
      cl25637
      Location:310 → 363
      DFRP_C; DRG Family Regulatory Proteins, Tma46

    6. NM_017722.5 → NP_060192.1  tRNA (guanine(26)-N(2))-dimethyltransferase isoform 1

      See identical proteins and their annotated locations for NP_060192.1

      Status: REVIEWED

      Source sequence(s)
      AC005546, BC040126, DC313999
      Consensus CDS
      CCDS12293.1
      UniProtKB/Swiss-Prot
      O76103, Q548Y5, Q8WVA6, Q9NXH9
      UniProtKB/TrEMBL
      A8K8L2
      Related
      ENSP00000416149.1, ENST00000437766.5
      Conserved Domains (3) summary
      smart00356
      Location:600 → 626
      ZnF_C3H1; zinc finger
      pfam02005
      Location:45 → 500
      TRM; N2,N2-dimethylguanosine tRNA methyltransferase
      cl25637
      Location:571 → 624
      DFRP_C; DRG Family Regulatory Proteins, Tma46

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      13104907..13116740 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      13230119..13241953 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NXH9.1 GenPept UniProtKB/Swiss-Prot:Q9NXH9

    Gene LinkOut

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

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