TRMT9B

protein-coding

tRNA methyltransferase 9B (putative), the group of 7BS DNA/RNA methyltransferases

Gene summary

Enables tRNA methyltransferase activity. Predicted to be involved in tRNA methylation and tRNA wobble uridine modification. Predicted to be active in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C8orf79
KIAA1456

MANE transcript

NM_020844.3

Inheritance

—

ClinVar variants

U:129B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.62

Max pathogenic AF

—

Genomic locus

chr8:12,945,642-13,031,503

External References & Databases

Ensembl (ENSG00000250305)

Transcript & Mutation Effects

hg38 • Region Span ~85.9 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 TRMT9B variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 134

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020844.3. 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			128 clinvar	6 clinvar		134
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	129	6	0	135

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 47 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020844.3	RefSeq	NP_065895.2	3	MANE Select
ENST00000524591.7	Ensembl	ENSP00000432695.1	3	MANE Select
NM_001099677.1	RefSeq	NP_001093147.1	1	Standard
ENST00000400069.7	Ensembl	ENSP00000468715.1	1	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 wobble uridine modification
tRNA modification
tRNA methylation
oxidation-reduction process

Molecular Function

tRNA binding
tRNA methyltransferase activity
tRNA (uracil) methyltransferase activity
2-oxoglutarate-dependent dioxygenase activity

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000524591
Coding exons: 3
Length: 85862
Individuals with no LoFs: 124511
Homozygous LoFs: 10
Heterozygous LoFs: 120
Defined: 124641
p: 0.000522

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-4.44	445	248	1.79	0.0000131	2996
Missense (PolyPhen)		133	92.259	1.4416		1067
Synonymous	-4.85	149	90.4	1.65	0.00000496	835
Loss of Function	-1.49	11	6.80	1.62	2.88e-7	84

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0023	0.0018	notable
Latino/Admixed American	0.00064	0.00058	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00028	0.00028	rare
Finnish	0.00023	0.00019	rare
European (Non-Finnish)	0.00046	0.00044	rare
South Asian	0.00056	0.00056	rare
Other	0.00050	0.00050	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May modifie wobble uridines in specific arginine and glutamic acid tRNAs. Acts as a tumor suppressor by promoting the expression of LIN9. {ECO:0000269|PubMed:23381944}.;

Recessive Scores

pRec: 0.0881

Intolerance Scores

RVIS EVS: 0.43
RVIS percentile EVS: 77.31

Essentials

Essential (gene trap): N