TRMT10B

protein-coding

tRNA methyltransferase 10B, the group of SPOUT methyltransferase domain containing

Gene summary

Enables tRNA (guanosine(9)-N1)-methyltransferase activity. Involved in protein insertion into mitochondrial inner membrane. Located in cytosol and mitochondrial inner membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

RG9MTD3

MANE transcript

NM_144964.4

Inheritance

—

ClinVar variants

U:53B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.62

Max pathogenic AF

—

Genomic locus

chr9:37,753,803-37,778,972

External References & Databases

Ensembl (ENSG00000165275)

Transcript & Mutation Effects

hg38 • Region Span ~25.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TRMT10B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 48

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144964.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			48 clinvar	4 clinvar		52
nonsense			1 clinvar	1 clinvar		2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	53	6	0	59

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 59 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144964.4	RefSeq	NP_659401.2	8	MANE Select
ENST00000297994.4	Ensembl	ENSP00000297994.3	8	MANE Select
NM_001286950.2	RefSeq	NP_001273879.1	7	Standard
NM_001286951.2	RefSeq	NP_001273880.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

tRNA methylation

Molecular Function

tRNA binding
tRNA (guanine-N1-)-methyltransferase activity
tRNA (guanine(9)-N(1))-methyltransferase activity

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000297994
Coding exons: 8
Length: 25166
Individuals with no LoFs: 123667
Homozygous LoFs: 18
Heterozygous LoFs: 1114
Defined: 124799
p: 0.00455

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.298	151	162	0.934	0.00000839	2045
Missense (PolyPhen)		32	31.116	1.0284		394
Synonymous	-0.225	61	58.8	1.04	0.00000307	569
Loss of Function	1.49	11	17.8	0.620	9.02e-7	225

Population LoF Frequency

Population	CAF	p-value	Status
African	0.033	0.032	notable
Latino/Admixed American	0.0019	0.0018	notable
Ashkenazi Jewish	0.00070	0.00070	rare
East Asian	0.00039	0.00039	rare
Finnish	0.0090	0.0089	notable
European (Non-Finnish)	0.0026	0.0026	notable
South Asian	0.0019	0.0018	notable
Other	0.0033	0.0033	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: 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). Probably not able to catalyze formation of N(1)-methyladenine at position 9 (m1A9) in tRNAs (PubMed:23042678). {ECO:0000269|PubMed:23042678}.;

Intolerance Scores

RVIS EVS: 0.22
RVIS percentile EVS: 68.13

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium