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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	55621
Gene name Gene Name - the full gene name approved by the HGNC.	TRNA methyltransferase 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	TRMT1
Synonyms (NCBI Gene) Gene synonyms aliases	MRT68, TRM1, hTRM1
Chromosome Chromosome number	19
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	19p13.13
Summary Summary of gene provided in NCBI Entrez Gene.	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

Protein

UniProt ID

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

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Intellectual Developmental Disorder	intellectual developmental disorder, autosomal recessive 68	rs1203487591, rs542184779, rs868289171, rs746572548, rs1568361011	N/A

Show/Hide Unknown Diseases (1)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Mental retardation	syndromic intellectual disability	N/A	N/A	GenCC

Show/Hide Text Mining Associations (6)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Breast Neoplasms	Associate	35021009
Developmental Disabilities	Associate	31898845
Drug Related Side Effects and Adverse Reactions	Associate	36190452
Epilepsy	Associate	31898845
Intellectual Disability	Associate	26308914, 28784718, 31898845
Mental Retardation Autosomal Recessive 4	Associate	26308914

TRMT1 (tRNA methyltransferase 1)