TRMT10A tRNA methyltransferase 10A [Homo sapiens (human)] - Gene

Summary

Official Symbol: TRMT10Aprovided by HGNC
Official Full Name: tRNA methyltransferase 10Aprovided by HGNC
Primary source: HGNC:HGNC:28403
See related: Ensembl:ENSG00000145331 MIM:616013; AllianceGenome:HGNC:28403
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: MSSGM; TRM10; MSSGM1; RG9MTD2; HEL-S-88
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 metabolism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
Expression: Ubiquitous expression in testis (RPKM 4.1), thyroid (RPKM 2.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4q23

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (99546711..99564039, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (102861479..102878808, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (100467868..100485196, complement)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Functional characterization of the human tRNA methyltransferases TRMT10A and TRMT10B.
Title: Functional characterization of the human tRNA methyltransferases TRMT10A and TRMT10B.
transcripts with increased m(6)A upon TRMT10A ablation contain an overrepresentation of m(1)G9-containing tRNAs codons read by tRNA(Gln(TTG)), tRNA(Arg(CCG)), and tRNA(Thr(CGT)) These findings collectively reveal the presence of coordinated mRNA and tRNA methylations and demonstrate a mechanism for regulating gene expression through the interactions between mRNA and tRNA modifying enzymes.
Title: Coordination of mRNA and tRNA methylations by TRMT10A.
demonstrate that human TRMT10A (hTRMT10A) and human TRMT10B (hTRMT10B) are not biochemically redundant
Title: Distinct substrate specificities of the human tRNA methyltransferases TRMT10A and TRMT10B.
tRNA guanosine 9 hypomethylation leads to tRNAGln fragmentation and that 5'-tRNAGln fragments mediate TRMT10A deficiency-induced beta-cell death. This study unmasks tRNA hypomethylation and fragmentation as a hitherto unknown mechanism of pancreatic beta-cell demise relevant to monogenic and polygenic forms of diabetes.
Title: Pancreatic β-cell tRNA hypomethylation and fragmentation link TRMT10A deficiency with diabetes.
A homozygous G to T transition in exon 2 of gene TRMT10A at nucleotide position 79 of the coding sequence was identified in a family with young-adult onset diabetes with intellectual disability, microcephaly and epilepsy.
Title: tRNA methyltransferase homologue gene TRMT10A mutation in young adult-onset diabetes with intellectual disability, microcephaly and epilepsy.
Homozygous deletion of TRMT10A is associated with a syndrome of failure to thrive, delayed puberty, intellectual disability and diabetes mellitus.
Title: Homozygous deletion of TRMT10A as part of a contiguous gene deletion in a syndrome of failure to thrive, delayed puberty, intellectual disability and diabetes mellitus.
TRMT10A dysfunction is associated with abnormalities in glucose homeostasis, short stature and microcephaly.
Title: TRMT10A dysfunction is associated with abnormalities in glucose homeostasis, short stature and microcephaly.
This is the first study describing the impact of TRMT10A deficiency in mammals, highlighting a role in the pathogenesis of microcephaly and early onset diabetes.
Title: tRNA methyltransferase homolog gene TRMT10A mutation in young onset diabetes and primary microcephaly in humans.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Microcephaly, short stature, and impaired glucose metabolism 1 MedGen: C4014997 OMIM: 616033 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH102787 (e-PCR)
- UniSTS:97121

STS-AA001648 (e-PCR)
- UniSTS:48347

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables tRNA (guanosine(9)-N1)-methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables tRNA (guanosine(9)-N1)-methyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables tRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables tRNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in tRNA N1-guanine methylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in tRNA N1-guanine methylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in tRNA methylation	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in actin cytoskeleton	IDA Inferred from Direct Assay more info
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: tRNA methyltransferase 10 homolog A

Names: RNA (guanine-9-)-methyltransferase domain-containing protein 2; epididymis secretory protein Li 88; tRNA (guanine(9)-N(1))-methyltransferase TRMT10A

NP_001128137.1

EC 2.1.1.221

NP_001128138.1

EC 2.1.1.221

NP_001362809.1

EC 2.1.1.221

NP_001362810.1

EC 2.1.1.221

NP_001362811.1

EC 2.1.1.221

NP_689505.1

EC 2.1.1.221

XP_047272374.1

EC 2.1.1.221

XP_054207242.1

EC 2.1.1.221

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_041774.1 RefSeqGene

Range

5019..22347

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001134665.3 → NP_001128137.1 tRNA methyltransferase 10 homolog A isoform 1

See identical proteins and their annotated locations for NP_001128137.1

Status: REVIEWED

Source sequence(s)

AC083902, AK313548, AW242551, BC028373, DB455183

Consensus CDS

CCDS3650.1

UniProtKB/Swiss-Prot

B2R8X7, Q8TBZ6, Q9Y2T9

UniProtKB/TrEMBL

A0A024RDJ9, V9HVY8

Related

ENSP00000378342.2, ENST00000394876.7

Conserved Domains (1) summary

cd18101
Location:101 → 276

Trm10euk_A; eukaryotic tRNA m1G9 methyltransferase Trm10 homolog A
NM_001134666.3 → NP_001128138.1 tRNA methyltransferase 10 homolog A isoform 1

See identical proteins and their annotated locations for NP_001128138.1

Status: REVIEWED

Source sequence(s)

AC083902, AK000332, AW242551, BC028373, DB455183

Consensus CDS

CCDS3650.1

UniProtKB/Swiss-Prot

B2R8X7, Q8TBZ6, Q9Y2T9

UniProtKB/TrEMBL

A0A024RDJ9, V9HVY8

Related

ENSP00000378343.3, ENST00000394877.7

Conserved Domains (1) summary

cd18101
Location:101 → 276

Trm10euk_A; eukaryotic tRNA m1G9 methyltransferase Trm10 homolog A
NM_001375880.1 → NP_001362809.1 tRNA methyltransferase 10 homolog A isoform 1

Status: REVIEWED

Source sequence(s)

AC083902

Consensus CDS

CCDS3650.1

UniProtKB/Swiss-Prot

B2R8X7, Q8TBZ6, Q9Y2T9

UniProtKB/TrEMBL

A0A024RDJ9, V9HVY8

Conserved Domains (1) summary

cd18101
Location:101 → 276

Trm10euk_A; eukaryotic tRNA m1G9 methyltransferase Trm10 homolog A
NM_001375881.1 → NP_001362810.1 tRNA methyltransferase 10 homolog A isoform 1

Status: REVIEWED

Source sequence(s)

AC083902

Consensus CDS

CCDS3650.1

UniProtKB/Swiss-Prot

B2R8X7, Q8TBZ6, Q9Y2T9

UniProtKB/TrEMBL

A0A024RDJ9, V9HVY8

Conserved Domains (1) summary

cd18101
Location:101 → 276

Trm10euk_A; eukaryotic tRNA m1G9 methyltransferase Trm10 homolog A
NM_001375882.1 → NP_001362811.1 tRNA methyltransferase 10 homolog A isoform 2

Status: REVIEWED

Source sequence(s)

AC083902

Conserved Domains (1) summary

cd18101
Location:101 → 269

Trm10euk_A; eukaryotic tRNA m1G9 methyltransferase Trm10 homolog A
NM_152292.5 → NP_689505.1 tRNA methyltransferase 10 homolog A isoform 1

See identical proteins and their annotated locations for NP_689505.1

Status: REVIEWED

Source sequence(s)

AC083902, AW242551, BC028373

Consensus CDS

CCDS3650.1

UniProtKB/Swiss-Prot

B2R8X7, Q8TBZ6, Q9Y2T9

UniProtKB/TrEMBL

A0A024RDJ9, V9HVY8

Related

ENSP00000273962.3, ENST00000273962.7

Conserved Domains (1) summary

cd18101
Location:101 → 276

Trm10euk_A; eukaryotic tRNA m1G9 methyltransferase Trm10 homolog A

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

99546711..99564039 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047416418.1 → XP_047272374.1 tRNA methyltransferase 10 homolog A isoform X1

UniProtKB/Swiss-Prot

B2R8X7, Q8TBZ6, Q9Y2T9

UniProtKB/TrEMBL

A0A024RDJ9, V9HVY8

Alternate T2T-CHM13v2.0

Genomic

NC_060928.1 Alternate T2T-CHM13v2.0

Range

102861479..102878808 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054351267.1 → XP_054207242.1 tRNA methyltransferase 10 homolog A isoform X1

UniProtKB/Swiss-Prot

B2R8X7, Q8TBZ6, Q9Y2T9

UniProtKB/TrEMBL

A0A024RDJ9, V9HVY8