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 metabolism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014] See more...

Aliases for TRMT10A Gene

Aliases for TRMT10A Gene

  • TRNA Methyltransferase 10A 2 3 5
  • RNA (Guanine-9-)-Methyltransferase Domain-Containing Protein 2 3 4
  • TRNA (Guanine(9)-N(1))-Methyltransferase TRMT10A 3 4
  • TRNA Methyltransferase 10 Homolog A 3 4
  • RG9MTD2 3 4
  • TRM10 2 3
  • RNA (Guanine-9-) Methyltransferase Domain Containing 2 2
  • TRNA Methyltransferase 10 Homolog A (S. Cerevisiae) 2
  • Epididymis Secretory Protein Li 88 3
  • EC 2.1.1.221 4
  • HEL-S-88 3
  • MGC27034 2
  • TRMT10A 5
  • MSSGM1 3
  • MSSGM 3

External Ids for TRMT10A Gene

Previous HGNC Symbols for TRMT10A Gene

  • RG9MTD2

Previous GeneCards Identifiers for TRMT10A Gene

  • GC04M100468

Summaries for TRMT10A Gene

Entrez Gene Summary for TRMT10A Gene

  • 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 metabolism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]

GeneCards Summary for TRMT10A Gene

TRMT10A (TRNA Methyltransferase 10A) is a Protein Coding gene. Diseases associated with TRMT10A include Microcephaly, Short Stature, And Impaired Glucose Metabolism 1 and Primary Microcephaly-Mild Intellectual Disability-Young-Onset Diabetes Syndrome. Among its related pathways are tRNA processing and Gene Expression. Gene Ontology (GO) annotations related to this gene include tRNA binding. An important paralog of this gene is TRMT10B.

UniProtKB/Swiss-Prot Summary for TRMT10A Gene

  • 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 at position 9 (m1A9) in tRNAs (PubMed:23042678).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TRMT10A Gene

Genomics for TRMT10A Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for TRMT10A Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TRMT10A on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TRMT10A

Genomic Locations for TRMT10A Gene

Latest Assembly
chr4:99,546,709-99,564,039
(GRCh38/hg38)
Size:
17,331 bases
Orientation:
Minus strand

Previous Assembly
chr4:100,467,868-100,485,196
(GRCh37/hg19 by Entrez Gene)
Size:
17,329 bases
Orientation:
Minus strand

chr4:100,467,866-100,485,189
(GRCh37/hg19 by Ensembl)
Size:
17,324 bases
Orientation:
Minus strand

Genomic View for TRMT10A Gene

Genes around TRMT10A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRMT10A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRMT10A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TRMT10A Gene

Proteins for TRMT10A Gene

  • Protein details for TRMT10A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TBZ6-TM10A_HUMAN
    Recommended name:
    tRNA methyltransferase 10 homolog A
    Protein Accession:
    Q8TBZ6
    Secondary Accessions:
    • B2R8X7
    • Q9Y2T9

    Protein attributes for TRMT10A Gene

    Size:
    339 amino acids
    Molecular mass:
    39719 Da
    Quaternary structure:
    • Interacts with tRNA.

    Three dimensional structures from OCA and Proteopedia for TRMT10A Gene

neXtProt entry for TRMT10A Gene

Post-translational modifications for TRMT10A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for TRMT10A Gene

Domains & Families for TRMT10A Gene

Gene Families for TRMT10A Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for TRMT10A Gene

Suggested Antigen Peptide Sequences for TRMT10A Gene

GenScript: Design optimal peptide antigens:
  • RNA (guanine-9-)-methyltransferase domain-containing protein 2 (RG9D2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8TBZ6

UniProtKB/Swiss-Prot:

TM10A_HUMAN :
  • Belongs to the class IV-like SAM-binding methyltransferase superfamily. TRM10 family.
Family:
  • Belongs to the class IV-like SAM-binding methyltransferase superfamily. TRM10 family.
genes like me logo Genes that share domains with TRMT10A: view

Function for TRMT10A Gene

Molecular function for TRMT10A Gene

UniProtKB/Swiss-Prot 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 at position 9 (m1A9) in tRNAs (PubMed:23042678).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=guanosine(9) in tRNA + S-adenosyl-L-methionine = H(+) + N(1)-methylguanosine(9) in tRNA + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:43156, Rhea:RHEA-COMP:10367, Rhea:RHEA-COMP:10368, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:73542, ChEBI:CHEBI:74269; EC=2.1.1.221; Evidence={ECO:0000269|PubMed:23042678, ECO:0000269|PubMed:25053765};.

Enzyme Numbers (IUBMB) for TRMT10A Gene

Phenotypes From GWAS Catalog for TRMT10A Gene

Gene Ontology (GO) - Molecular Function for TRMT10A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000049 tRNA binding IBA,IDA 25053765
GO:0003723 RNA binding HDA 22658674
GO:0005515 protein binding IPI 32296183
GO:0008168 methyltransferase activity IEA --
GO:0009019 tRNA (guanine-N1-)-methyltransferase activity IDA 23042678
genes like me logo Genes that share ontologies with TRMT10A: view
genes like me logo Genes that share phenotypes with TRMT10A: view

Human Phenotype Ontology for TRMT10A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for TRMT10A Gene

MGI Knock Outs for TRMT10A:
  • Trmt10a Trmt10a<tm1a(EUCOMM)Wtsi>

Animal Models for research

  • Taconic Biosciences Mouse Models for TRMT10A

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRMT10A

No data available for Transcription Factor Targets and HOMER Transcription for TRMT10A Gene

Localization for TRMT10A Gene

Subcellular locations from UniProtKB/Swiss-Prot for TRMT10A Gene

Nucleus. Nucleus, nucleolus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TRMT10A gene
Compartment Confidence
nucleus 5
extracellular 4
cytoskeleton 4
cytosol 4
mitochondrion 3
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Nucleoplasm (3)
  • Actin filaments (1)
  • Cytosol (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for TRMT10A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,IDA 24204302
GO:0005654 nucleoplasm IDA --
GO:0005730 nucleolus IDA 24204302
GO:0005739 mitochondrion IEA --
GO:0005829 cytosol IDA 23042678
genes like me logo Genes that share ontologies with TRMT10A: view

Pathways & Interactions for TRMT10A Gene

PathCards logo

SuperPathways for TRMT10A Gene

genes like me logo Genes that share pathways with TRMT10A: view

Pathways by source for TRMT10A Gene

Gene Ontology (GO) - Biological Process for TRMT10A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002939 tRNA N1-guanine methylation IMP 32392304
GO:0030488 tRNA methylation IEA,IDA 25053765
GO:0032259 methylation IEA --
GO:0090646 mitochondrial tRNA processing IBA 21873635
genes like me logo Genes that share ontologies with TRMT10A: view

No data available for SIGNOR curated interactions for TRMT10A Gene

Drugs & Compounds for TRMT10A Gene

No Compound Related Data Available

Transcripts for TRMT10A Gene

mRNA/cDNA for TRMT10A Gene

6 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TRMT10A

Alternative Splicing Database (ASD) splice patterns (SP) for TRMT10A Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8
SP1:
SP2:
SP3: -
SP4: - -
SP5: -

Relevant External Links for TRMT10A Gene

GeneLoc Exon Structure for
TRMT10A

Expression for TRMT10A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TRMT10A Gene

Protein differential expression in normal tissues from HIPED for TRMT10A Gene

This gene is overexpressed in Lung (25.0), Fetal ovary (16.2), Peripheral blood mononuclear cells (16.2), and Lymph node (6.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TRMT10A Gene



Protein tissue co-expression partners for TRMT10A Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TRMT10A

SOURCE GeneReport for Unigene cluster for TRMT10A Gene:

Hs.380412

mRNA Expression by UniProt/SwissProt for TRMT10A Gene:

Q8TBZ6-TM10A_HUMAN
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 not in dorsal telencephalon, at later stages.

Phenotype-based relationships between genes and organs from Gene ORGANizer for TRMT10A Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • face
  • head
  • neck
  • nose
  • skull
General:
  • spinal column
genes like me logo Genes that share expression patterns with TRMT10A: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Evidence on tissue expression from TISSUES for TRMT10A Gene

Orthologs for TRMT10A Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for TRMT10A Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia TRMT10A 30
  • 99.8 (n)
RG9MTD2 31
  • 93 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia TRMT10A 30 31
  • 90.43 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia TRMT10A 30 31
  • 89.02 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Trmt10a 30 17 31
  • 81.22 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Trmt10a 30
  • 80.04 (n)
Oppossum
(Monodelphis domestica)
Mammalia TRMT10A 31
  • 70 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia TRMT10A 31
  • 49 (a)
OneToOne
Chicken
(Gallus gallus)
Aves TRMT10A 30 31
  • 75.69 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia TRMT10A 31
  • 63 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia trmt10a 30
  • 67.72 (n)
Str.6891 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.15028 30
Zebrafish
(Danio rerio)
Actinopterygii LOC560222 30
  • 64.58 (n)
TRMT10A 31
  • 56 (a)
OneToOne
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7744 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000324 30
  • 45.44 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG14618 30 31
  • 43.51 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea F25H8.1 30 31
  • 53.48 (n)
OneToMany
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_ADR110C 30
  • 48.13 (n)
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C03740g 30
  • 48.06 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes TRM10 30 31 33
  • 45.16 (n)
OneToMany
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes trm10 30
  • 51.63 (n)
Bread mold
(Neurospora crassa)
Ascomycetes NCU02231 30
  • 46.67 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.7762 31
  • 36 (a)
OneToOne
Species where no ortholog for TRMT10A was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for TRMT10A Gene

ENSEMBL:
Gene Tree for TRMT10A (if available)
TreeFam:
Gene Tree for TRMT10A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TRMT10A: view image

Paralogs for TRMT10A Gene

Paralogs for TRMT10A Gene

genes like me logo Genes that share paralogs with TRMT10A: view

Variants for TRMT10A Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TRMT10A Gene

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
974899 Likely Pathogenic: Microcephaly, short stature, and impaired glucose metabolism 1 99,550,938(-) GG/TA
NM_001134665.3(TRMT10A):c.697_698delinsTA (p.Pro233Ter)
NONSENSE
984716 Uncertain Significance: Microcephaly, short stature, and impaired glucose metabolism 1 99,558,049(-) C/G
NM_001134665.3(TRMT10A):c.348G>C (p.Lys116Asn)
MISSENSE
rs10007569 Uncertain Significance: Microcephaly, short stature, and impaired glucose metabolism 1; not specified. - 99,557,367(-) C/Tp.Arg133Gln
NM_001134665.3(TRMT10A):c.398G>A (p.Arg133Gln)
MISSENSE
rs140905333 Likely Benign: not provided 99,550,971(-) G/A
NM_001134665.3(TRMT10A):c.665C>T (p.Ala222Val)
MISSENSE
rs142895837 Pathogenic: not provided 99,559,260(-) C/A
NM_001134665.3(TRMT10A):c.79G>T (p.Glu27Ter)
NONSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for TRMT10A Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for TRMT10A Gene

Variant ID Type Subtype PubMed ID
dgv51e213 CNV gain 24956385
esv3584519 CNV gain 24956385
nsv474143 CNV novel sequence insertion 20440878

Variation tolerance for TRMT10A Gene

Residual Variation Intolerance Score: 55.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.24; 24.86% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TRMT10A Gene

Human Gene Mutation Database (HGMD)
TRMT10A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRMT10A

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRMT10A Gene

Disorders for TRMT10A Gene

MalaCards: The human disease database

(8) MalaCards diseases for TRMT10A Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

TM10A_HUMAN
  • Microcephaly, short stature, and impaired glucose metabolism 1 (MSSGM1) [MIM:616033]: A disease characterized by microcephaly, mental retardation, short stature, and disturbed glucose metabolism. Additional clinical features include delayed puberty, hypoglycemia-related seizures, hyperinsulinemic hypoglycemia, and early-onset diabetes. {ECO:0000269 PubMed:24204302, ECO:0000269 PubMed:25053765, ECO:0000269 PubMed:26526202, ECO:0000269 PubMed:26535115}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for TRMT10A

genes like me logo Genes that share disorders with TRMT10A: view

No data available for Genatlas for TRMT10A Gene

Publications for TRMT10A Gene

  1. tRNA methyltransferase homolog gene TRMT10A mutation in young onset diabetes and primary microcephaly in humans. (PMID: 24204302) Igoillo-Esteve M … Cnop M (PLoS genetics 2013) 2 3 4 74
  2. TRMT10A dysfunction is associated with abnormalities in glucose homeostasis, short stature and microcephaly. (PMID: 25053765) Gillis D … Elpeleg O (Journal of medical genetics 2014) 3 4 74
  3. A subcomplex of human mitochondrial RNase P is a bifunctional methyltransferase--extensive moonlighting in mitochondrial tRNA biogenesis. (PMID: 23042678) Vilardo E … Rossmanith W (Nucleic acids research 2012) 2 3 4
  4. Functional characterization of the human tRNA methyltransferases TRMT10A and TRMT10B. (PMID: 32392304) Vilardo E … Rossmanith W (Nucleic acids research 2020) 2 3
  5. tRNA methyltransferase homologue gene TRMT10A mutation in young adult-onset diabetes with intellectual disability, microcephaly and epilepsy. (PMID: 26526202) Yew TW … Pearson ER (Diabetic medicine : a journal of the British Diabetic Association 2016) 3 4

Products for TRMT10A Gene

Sources for TRMT10A Gene