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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
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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
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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)

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

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