Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
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

Show/Hide all (5)

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

Show/Hide all (4)

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

Show/Hide all (29)

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
GO:0003723	Function	RNA binding	IEA
GO:0005515	Function	Protein binding	IPI	16189514, 21044950, 21516116, 25416956, 32296183
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	28784718, 33499731, 38814682
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IDA	28784718, 33499731, 38814682
GO:0005737	Component	Cytoplasm	IEA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IDA	28784718, 33499731, 38814682
GO:0005739	Component	Mitochondrion	IEA
GO:0006400	Process	TRNA modification	IEA
GO:0006400	Process	TRNA modification	TAS
GO:0008033	Process	TRNA processing	IEA
GO:0008168	Function	Methyltransferase activity	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0016423	Function	TRNA (guanine) methyltransferase activity	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0032259	Process	Methylation	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0160104	Function	TRNA (guanine(26)-N2)-dimethyltransferase activity	EXP	10982862
GO:0160104	Function	TRNA (guanine(26)-N2)-dimethyltransferase activity	IDA	28784718, 37204604, 39786990
GO:0160104	Function	TRNA (guanine(26)-N2)-dimethyltransferase activity	IEA
GO:0160104	Function	TRNA (guanine(26)-N2)-dimethyltransferase activity	IMP	31898845

MIM	HGNC	e!Ensembl
611669	25980	ENSG00000104907

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
PF02005	TRM	45 → 500	N2,N2-dimethylguanosine tRNA methyltransferase	Family
PF00642	zf-CCCH	601 → 626	Zinc finger C-x8-C-x5-C-x3-H type (and similar)	Family

Sequence

MQGSSLWLSLTFRSARVLSRARFFEWQSPGLPNTAAMENGTGPYGEERPREVQETTVTEG
AAKIAFPSANEVFYNPVQEFNRDLTCAVITEFARIQLGAKGIQIKVPGEKDTQKVVVDLS
EQEEEKVELKESENLASGDQPRTAAVGEICEEGLHVLEGLAASGLRSIRFALEVPGLRSV
VANDASTRAVDLIRRNVQLNDVAHLVQPSQADARMLMYQHQRVSERFDVIDLDPYGSPAT
FLDAAVQAVSEGGLLCVTCTDMAVLAGNSGETCYSKYGAMALKSRACHEMALRIVLHSLD
LRANCYQRFVVPLLSISADFYVRVFVRVFTGQAKVKASASKQALVFQCVGCGAFHLQRLG
KASGVPSGRAKFSAACGPPVTPECEHCGQRHQLGGPMWAEPIHDLDFVGRVLEAVSANPG
RFHTSERIRGVLSVITEELPDVPLYYTLDQLSSTIHCNTPSLLQLRSALLHADFRVSLSH
ACKNAVKTDAPASALWDIMRCWEKECPVKRERLSETSPAFRILSVEPRLQANFTIREDAN
PSSRQRGLKRFQANPEANWGPRPRARPGGKAADEAMEERRRLLQNKRKEPPEDVAQRAAR
LKTFPCKRFKEGTCQRGDQCCYSHSPPTPRVSADAAPDCPETSNQTPPGPGAAAGPGID

Sequence length

659

Interactions

View interactions

	Reactome
			tRNA modification in the nucleus and cytosol

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)

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Intellectual developmental disorder, autosomal recessive 68	Likely pathogenic; Pathogenic	rs2019344087, rs2019322057, rs2145578013, rs2513108777, rs542184779, rs1352655452, rs750785552, rs756963751, rs763302328, rs2513068920, rs868289171, rs746572548, rs1568361011, rs1203487591, rs2019321826, rs751298016 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)

Show/Hide Unknown Diseases (7)

Phenotype Name	Clinical Significance	Source	Evidence Score
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.
Colon adenocarcinoma	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTELLECTUAL DISABILITY	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MENTAL RETARDATION	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SPECIFIC SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet, Orphanet Disgenet, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TRMT1-related disorder	Likely benign; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

TRMT1 (tRNA methyltransferase 1)