TRMT2A

protein-coding

tRNA methyltransferase 2 homolog A, the group of 7BS DNA/RNA methyltransferases|MicroRNA protein coding host genes

Gene summary

The protein encoded by this gene is of unknown function. However, it is orthologous to the mouse Trmt2a gene and contains an RNA methyltransferase domain. Expression of this gene varies during the cell cycle, with aberrant expression being a possible biomarker in certain breast cancers. Several transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

MANE transcript

NM_022727.6

Inheritance

—

ClinVar variants

U:128B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.61

Max pathogenic AF

—

Genomic locus

chr22:20,111,875-20,117,392

External References & Databases

Ensembl (ENSG00000099899)

Transcript & Mutation Effects

hg38 • Region Span ~5.5 kb

Loading mutation effect viewer...

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 TRMT2A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 115

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022727.6. 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			4 clinvar	2 clinvar		6
missense			120 clinvar	2 clinvar		122
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	128	4	0	132

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 46 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022727.6	RefSeq	NP_073564.3	12	MANE Select
ENST00000252136.12	Ensembl	ENSP00000252136.7	12	MANE Select
NM_001257994.2	RefSeq	NP_001244923.1	12	Standard
NM_001331039.2	RefSeq	NP_001317968.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

RNA methylation
RNA processing

Molecular Function

RNA binding
RNA methyltransferase activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000252136
Coding exons: 12
Length: 5527
Individuals with no LoFs: 125675
Homozygous LoFs: 1
Heterozygous LoFs: 69
Defined: 125745
p: 0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.132	405	398	1.02	0.0000254	4008
Missense (PolyPhen)		95	95.756	0.99211		940
Synonymous	-2.01	208	174	1.19	0.0000117	1315
Loss of Function	1.88	17	27.7	0.614	0.00000152	290

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00050	0.00049	rare
Latino/Admixed American	0.00056	0.00055	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.000049	0.000046	rare
European (Non-Finnish)	0.00023	0.00022	rare
South Asian	0.00047	0.00042	rare
Other	0.00018	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in nucleic acid metabolism and/or modifications.;

Recessive Scores

pRec: 0.101

Intolerance Scores

LoFtool: 0.907
RVIS EVS: -0.95
RVIS percentile EVS: 9.32

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 1.00

Gene Damage Prediction

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