TRMT1 (tRNA methyltransferase 1)

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Gene Gene information from NCBI Gene database.
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Entrez ID 55621
Gene name TRNA methyltransferase 1
Gene symbol TRMT1
Synonyms (NCBI Gene)
MRT68TRM1hTRM1
Chromosome 19
Chromosome location 19p13.13
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 methion
SNPs SNP information provided by dbSNP.
5
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SNP ID Visualize variation Clinical significance Consequence
rs542184779 G>A Likely-pathogenic Coding sequence variant, non coding transcript variant, missense variant
rs746572548 ACGTCAAACCTCTCCGACACCCTCTGGTGCTG>- Pathogenic 5 prime UTR variant, frameshift variant, coding sequence variant, non coding transcript variant
rs1203487591 CA>- Pathogenic Frameshift variant, coding sequence variant, non coding transcript variant
rs1555716802 T>C Likely-pathogenic Splice acceptor variant
rs1568361011 C>A Pathogenic Splice donor variant
miRNA miRNA information provided by mirtarbase database.
4
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miRTarBase ID miRNA Experiments Reference
MIRT001584 hsa-let-7b-5p pSILAC 18668040
MIRT020603 hsa-miR-155-5p Proteomics 18668040
MIRT031488 hsa-miR-16-5p Proteomics 18668040
MIRT001584 hsa-let-7b-5p Proteomics;Other 18668040
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
29 Show/Hide all (29)
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GO ID Ontology Definition Evidence Reference
GO:0000049 Function TRNA binding IEA
GO:0002940 Process TRNA N2-guanine methylation IBA
GO:0002940 Process TRNA N2-guanine methylation IDA 28784718, 37204604, 39786990
GO:0002940 Process TRNA N2-guanine methylation IMP 31898845
GO:0003723 Function RNA binding HDA 22658674
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
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MIM HGNC e!Ensembl
611669 25980 ENSG00000104907
Protein Protein information from UniProt database.
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UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q9NXH9
Protein name tRNA (guanine(26)-N(2))-dimethyltransferase (EC 2.1.1.216) (tRNA 2,2-dimethylguanosine-26 methyltransferase) (tRNA methyltransferase 1) (hTRM1) (tRNA(guanine-26,N(2)-N(2)) methyltransferase) (tRNA(m(2,2)G26)dimethyltransferase)
Protein function Dimethylates a single guanine residue at position 26 of most nuclear- and mitochondrial-encoded tRNAs using S-adenosyl-L-methionine as donor of the methyl groups (PubMed:10982862, PubMed:28784718, PubMed:37204604, PubMed:39786990). tRNA guanine(
PDB 9DW6
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00642 zf-CCCH 601 → 626 Zinc finger C-x8-C-x5-C-x3-H type (and similar) Family
PF02005 TRM 45 → 500 N2,N2-dimethylguanosine tRNA methyltransferase Family
Sequence 
MQGSSLWLSLTFRSARVLSRARFFEWQSPGLPNTAAMENGTGPYGEERPREVQETTVTEG
AAKIAFPSANEVFYNPVQEFNRDLTCAVITEFARIQLGAKGIQIKVPGEKDTQKVVVDLS
EQEEEKVELKESENLASGDQPRTAAVGEICEEGLHVLEGLAASGLRSIRFALEVPGLRSV
VANDASTRAVDLIRRNVQLNDVAHLVQPSQADARMLMYQHQRVSERFDVIDLDPYGSPAT
FLDAAVQAVSEGGLLCVTCTDMAVLAGNSGETCYSKYGAMALKSRACHEMALRIVLHSLD
LRANCYQRFVVPLLSISADFYVRVFVRVFTGQAKVKASASKQALVFQCVGCGAFHLQRLG
KASGVPSGRAKFSAACGPPVTPECEHCGQRHQLGGPMWAEPIHDLDFVGRVLEAVSANPG
RFHTSERIRGVLSVITEELPDVPLYYTLDQLSSTIHCNTPSLLQLRSALLHADFRVSLSH
ACKNAVKTDAPASALWDIMRCWEKECPVKRERLSETSPAFRILSVEPRLQANFTIREDAN
PSSRQRGLKRFQANPEANWGPRPRARPGGKAADEAMEERRRLLQNKRKEPPEDVAQRAAR
LKTFPCKRFKEGTCQRGDQCCYSHSPPTPRVSADAAPDCPETSNQTPPGPGAAAGPGID
Sequence length 659
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
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Reactome Pathway
tRNA modification in the nucleus and cytosol
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
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Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Intellectual developmental disorder, autosomal recessive 68 Likely pathogenic; Pathogenic rs2019344087, rs2019322057, rs2145578013, rs2513108777, rs542184779, rs1352655452, rs750785552, rs756963751, rs763302328, rs2513068920, rs868289171, rs746572548, rs1568361011, rs1203487591, rs2019321826
View all (1 more)		 RCV001788536
RCV001797563
RCV001823658
RCV003156053
RCV003987404
View all (11 more)
★★★★★
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Squamous cell carcinoma of the head and neck Likely pathogenic rs542184779 RCV005889666
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Show/Hide Unknown Diseases (8)
Phenotype Name Clinical Significance Source Reference Evidence Score
Colon adenocarcinoma Uncertain significance ClinVar —
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
complex neurodevelopmental disorder — ClinGen ClinGen report
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
INTELLECTUAL DISABILITY — CTD 21937992
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Lung cancer Uncertain significance ClinVar —
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
MENTAL RETARDATION — Disgenet 21937992
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
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MED13 1 shared diseasecomplex neurodevelopmental disorder 5 shared evidence sourcesClinVar (Intellectual developmental disorder), GenCC (Intellectual developmental disorder), HPO (Intellectual developmental disorder), Orphanet (Non-specific syndromic intellectual disability), ClinGen (complex neurodevelopmental disorder) Related via 1 shared disease including complex neurodevelopmental disorder — evidence mostly ClinVar. NAA15 5 shared evidence sourcesClinVar (Intellectual developmental disorder), GenCC (Intellectual developmental disorder), HPO (Intellectual developmental disorder), CTD (Intellectual developmental disorder), Orphanet (Non-specific syndromic intellectual disability) Related via 5 shared evidence sources. HNRNPC 3 shared evidence sourcesClinVar (Intellectual developmental disorder), HPO (Intellectual developmental disorder), Orphanet (Non-specific syndromic intellectual disability) Related via 3 shared evidence sources. WASHC4 4 shared evidence sourcesClinVar (Intellectual developmental disorder), GenCC (Intellectual developmental disorder), HPO (Intellectual developmental disorder), CTD (Intellectual developmental disorder) Related via 4 shared evidence sources. CACNG2 1 shared diseasecomplex neurodevelopmental disorder 5 shared evidence sourcesClinVar (Intellectual developmental disorder), GenCC (Intellectual developmental disorder), HPO (Intellectual developmental disorder), CTD (Intellectual developmental disorder), ClinGen (complex neurodevelopmental disorder) Related via 1 shared disease including complex neurodevelopmental disorder — evidence mostly ClinVar.
Neurodevelopmental disorder Linked via 3 of 5 related genesMED13, NAA15, CACNG2 Autism Linked via 2 of 5 related genesMED13, NAA15 Nonsyndromic intellectual disability Linked via 2 of 5 related genesWASHC4, CACNG2 Schizophrenia Linked via 2 of 5 related genesWASHC4, CACNG2 Alzheimer disease Linked via 1 of 5 related genesMED13