TRMT61A

protein-coding

tRNA methyltransferase 61A, the group of 7BS DNA/RNA methyltransferases

Gene summary

Enables mRNA (adenine-N1-)-methyltransferase activity. Involved in mRNA processing. Predicted to be located in nucleoplasm. Predicted to be part of tRNA (m1A) methyltransferase complex. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C14orf172

MANE transcript

NM_152307.3

Inheritance

—

ClinVar variants

P:1U:43B:2

Top phenotype

De Lange syndrome

gnomAD constraint

pLI —, LoF o/e 0.42

Max pathogenic AF

—

Genomic locus

chr14:103,529,196-103,537,073

External References & Databases

Ensembl (ENSG00000166166)

Transcript & Mutation Effects

hg38 • Region Span ~7.9 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 TRMT61A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 45

De Lange syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152307.3. 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						0
missense		1 clinvar	43 clinvar	2 clinvar		46
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	43	2	0	46

Highest pathogenic variant AF is 0.00020854344

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152307.3	RefSeq	NP_689520.2	3	MANE Select
ENST00000389749.9	Ensembl	ENSP00000374399.4	3	MANE Select
ENST00000299202.4	Ensembl	ENSP00000299202.4	3	Standard
ENST00000896880.1	Ensembl	ENSP00000566939.1	3	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
mRNA methylation

Molecular Function

tRNA (adenine-N1-)-methyltransferase activity
mRNA (adenine-N1-)-methyltransferase activity

Cellular Component

nucleus
nucleoplasm
tRNA (m1A) methyltransferase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000389749
Coding exons: 3
Length: 7890
Individuals with no LoFs: 124960
Homozygous LoFs: 0
Heterozygous LoFs: 22
Defined: 124982
p: 0.0000880

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.28	160	212	0.753	0.0000155	1818
Missense (PolyPhen)		36	71.476	0.50366		624
Synonymous	0.253	92	95.1	0.967	0.00000730	641
Loss of Function	1.65	4	9.48	0.422	4.91e-7	91

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalytic subunit of tRNA (adenine-N(1)-)- methyltransferase, which catalyzes the formation of N(1)- methyladenine at position 58 (m1A58) in initiator methionyl-tRNA (PubMed:16043508). Catalytic subunit of mRNA N(1)- methyltransferase complex, which mediates methylation of adenosine residues at the N(1) position of a small subset of mRNAs: N(1) methylation takes place in tRNA T-loop-like structures of mRNAs and is only present at low stoichiometries (PubMed:29107537, PubMed:29072297). {ECO:0000269|PubMed:16043508, ECO:0000269|PubMed:29072297, ECO:0000269|PubMed:29107537}.;

Recessive Scores

pRec: 0.140

Intolerance Scores

LoFtool: 0.487
RVIS EVS: -0.67
RVIS percentile EVS: 15.62

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.689

Gene Damage Prediction

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