TRMT11

protein-coding

tRNA methyltransferase 11 homolog, the group of 7BS DNA/RNA methyltransferases

Gene summary

Enables tRNA (guanine(10)-N2)-methyltransferase activity. Predicted to be involved in RNA methylation. Located in mitochondrion. Part of tRNA (m2G10) methyltransferase complex. Is active in cytoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C6orf75

MANE transcript

NM_001031712.3

Inheritance

—

ClinVar variants

U:72B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr6:125,986,479-126,203,817

External References & Databases

Ensembl (ENSG00000066651)

Transcript & Mutation Effects

hg38 • Region Span ~217.3 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 TRMT11 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 72

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001031712.3. 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			70 clinvar	2 clinvar		72
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	72	2	0	74

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 87 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001031712.3	RefSeq	NP_001026882.2	13	MANE Select
ENST00000334379.11	Ensembl	ENSP00000333934.5	13	MANE Select
NM_001350580.2	RefSeq	NP_001337509.1	13	Standard
NM_001350581.2	RefSeq	NP_001337510.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

tRNA modification in the nucleus and cytosol
tRNA processing
Metabolism of RNA

Biological Process

tRNA methylation

Molecular Function

tRNA binding
tRNA (guanine-N2-)-methyltransferase activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000334379
Coding exons: 13
Length: 52847
Individuals with no LoFs: 125649
Homozygous LoFs: 0
Heterozygous LoFs: 99
Defined: 125748
p: 0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0239	242	243	0.996	0.0000118	3041
Missense (PolyPhen)		51	55.229	0.92343		720
Synonymous	-0.889	97	86.5	1.12	0.00000429	834
Loss of Function	1.08	21	27.1	0.776	0.00000131	349

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0014	0.0012	notable
Latino/Admixed American	0.00070	0.00067	rare
Ashkenazi Jewish	0.00072	0.00069	rare
East Asian	0.00033	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00022	0.00022	rare
South Asian	0.00056	0.00056	rare
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalytic subunit of an S-adenosyl-L-methionine- dependent tRNA methyltransferase complex that mediates the methylation of the guanosine nucleotide at position 10 (m2G10) in tRNAs. {ECO:0000250}.;

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.907
RVIS EVS: -0.18
RVIS percentile EVS: 40.45

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.972

Gene Damage Prediction

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