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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	93587
Gene name	TRNA methyltransferase 10A
Gene symbol	TRMT10A
Synonyms (NCBI Gene)	HEL-S-88MSSGMMSSGM1RG9MTD2TRM10
Chromosome	4
Chromosome location	4q23
Summary	This gene encodes a protein that belongs to the tRNA (Guanine-1)-methyltransferase family. A similar gene in yeast modifies several different tRNA species. Mutations in this gene are associated with microcephaly, short stature, and impaired glucose metabo

Show/Hide all (3)

SNP ID	Visualize variation	Clinical significance	Consequence
rs142895837	C>A	Pathogenic	Stop gained, coding sequence variant
rs587777743	G>A	Likely-pathogenic	Stop gained, coding sequence variant
rs587777744	C>T	Pathogenic	Missense variant, coding sequence variant

Show/Hide all (1)

miRTarBase ID	miRNA	Experiments	Reference
MIRT019687	hsa-miR-375	Microarray	20215506

Show/Hide all (24)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000049	Function	TRNA binding	IBA
GO:0000049	Function	TRNA binding	IDA	25053765
GO:0002939	Process	TRNA N1-guanine methylation	IBA
GO:0002939	Process	TRNA N1-guanine methylation	IMP	32392304
GO:0003723	Function	RNA binding	HDA	22658674
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	24204302
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IBA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005730	Component	Nucleolus	IDA	24204302
GO:0005730	Component	Nucleolus	IEA
GO:0005829	Component	Cytosol	IBA
GO:0005829	Component	Cytosol	IDA	23042678
GO:0008168	Function	Methyltransferase activity	IEA
GO:0015629	Component	Actin cytoskeleton	IDA
GO:0016740	Function	Transferase activity	IEA
GO:0030488	Process	TRNA methylation	IDA	25053765
GO:0032259	Process	Methylation	IEA
GO:0052905	Function	TRNA (guanosine(9)-N1)-methyltransferase activity	IDA	23042678
GO:0052905	Function	TRNA (guanosine(9)-N1)-methyltransferase activity	IEA
GO:0052905	Function	TRNA (guanosine(9)-N1)-methyltransferase activity	IMP	32392304
GO:0070062	Component	Extracellular exosome	HDA	19056867

MIM	HGNC	e!Ensembl
616013	28403	ENSG00000145331

Q8TBZ6

Protein name

tRNA methyltransferase 10 homolog A (EC 2.1.1.221) (RNA (guanine-9-)-methyltransferase domain-containing protein 2) (tRNA (guanine(9)-N(1))-methyltransferase TRMT10A)

Protein function

S-adenosyl-L-methionine-dependent guanine N(1)-methyltransferase that catalyzes the formation of N(1)-methylguanine at position 9 (m1G9) in tRNAs (PubMed:23042678, PubMed:25053765). Probably not able to catalyze formation of N(1)-methyladenine a

PDB

4FMW

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01746	tRNA_m1G_MT	110 → 276	tRNA (Guanine-1)-methyltransferase	Family

Tissue specificity

TISSUE SPECIFICITY: Expressed in embryonic and fetal brain. It is expressed throughout the dorsal telencephalon at 8 and 11 weeks of gestation, with highest expression in ventricular zone and marginal zone. Detected in cerebellar cortex and nuclei, but no

Sequence

MSSEMLPAFIETSNVDKKQGINEDQEESQKPRLGEGCEPISKRQMKKLIKQKQWEEQREL
RKQKRKEKRKRKKLERQCQMEPNSDGHDRKRVRRDVVHSTLRLIIDCSFDHLMVLKDIKK
LHKQIQRCYAENRRALHPVQFYLTSHGGQLKKNMDENDKGWVNWKDIHIKPEHYSELIKK
EDLIYLTSDSPNILKELDESKAYVIGGLVDHNHHKGLTYKQASDYGINHAQLPLGNFVKM
NSRKVLAVNHVFEIILEYLETRDWQEAFFTILPQRKGAVPTDKACESASHDNQSVRMEEG
GSDSDSSEEEYSRNELDSPHEEKQDKENHTESTVNSLPH

Sequence length

339

Interactions

View interactions

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
Abnormality of the nervous system	Likely pathogenic; Pathogenic	rs1314619609	RCV001814306	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Microcephaly, short stature, and impaired glucose metabolism 1	Pathogenic; Likely pathogenic	rs1383664881, rs1724246827, rs587777743, rs587777744, rs748994888, rs2476032136, rs2476027546, rs1723938282	RCV001806433 RCV005868488 RCV000144247 RCV000144248 RCV002290853 RCV002289180 RCV003152861 RCV001251196 View all (3 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (6)

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.
CONGENITAL NEUROLOGIC ANOMALIES	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LIVER DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-ALCOHOLIC FATTY LIVER DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PRIMARY MICROCEPHALY, MILD INTELLECTUAL DISABILITY, YOUNG-ONSET DIABETES SYNDROME	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PRIMARY MICROCEPHALY-MILD INTELLECTUAL DISABILITY-YOUNG-ONSET DIABETES SYNDROME	—	GWAS catalog, Orphanet GWAS catalog, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TRMT10A-related disorder	Benign; Conflicting classifications of pathogenicity; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (29)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Aphasia	Aphasia	Pubtator	33067246	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Clumsiness - motor delay	Motor delay	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	20459617	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes	Diabetes	BEFREE	24204302, 25053765, 26297882, 26526202, 30247717		★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes Mellitus	BEFREE	24204302, 25053765, 26297882, 26526202, 30247717		★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes mellitus	Pubtator	26526202, 33067246, 33448213	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus Type 2	Diabetes mellitus, type 2	Pubtator	26526202, 33067246	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	BEFREE	26526202		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	BEFREE	25053765		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	BEFREE	26526202		★★★★★ ★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	Pubtator	26526202, 33067246	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Growth Disorders	Growth disorder	Pubtator	33448213	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Insulin Resistance	Diabetes mellitus, type 2	Pubtator	33067246	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	25053765, 26526202		★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	26526202, 33067246, 33448213, 37949221	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Kidney disease	Pubtator	33448213	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	UNIPROT_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	BEFREE	24204302, 25053765, 26526202, 30247717		★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	Pubtator	26526202, 33067246, 33448213, 37949221	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
MICROCEPHALY, SHORT STATURE, AND IMPAIRED GLUCOSE METABOLISM 1	Microcephaly, Short Stature, And Impaired Glucose Metabolism	GENOMICS_ENGLAND_DG	24204302, 26297882, 26535115		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
MICROCEPHALY, SHORT STATURE, AND IMPAIRED GLUCOSE METABOLISM 1	Microcephaly, Short Stature, And Impaired Glucose Metabolism	UNIPROT_DG	24204302, 25053765, 26526202, 26535115		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
MICROCEPHALY, SHORT STATURE, AND IMPAIRED GLUCOSE METABOLISM 1	Microcephaly, Short Stature, And Impaired Glucose Metabolism	CTD_human_DG			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
MICROCEPHALY, SHORT STATURE, AND IMPAIRED GLUCOSE METABOLISM 1	Microcephaly, Short Stature, And Impaired Glucose Metabolism	CLINVAR_DG			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Primary microcephaly	Microcephaly	BEFREE	24204302		★★★★★ ★☆☆☆☆ Found in Text Mining only
Primary microcephaly	Microcephaly	GENOMICS_ENGLAND_DG	26535115		★★★★★ ★☆☆☆☆ Found in Text Mining only
Primary microcephaly-mild intellectual disability-young-onset diabetes syndrome	Microcephaly-Mild Intellectual Disability Diabetes Syndrome	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

TRMT10A (tRNA methyltransferase 10A)