TRMT2B

protein-coding

tRNA methyltransferase 2 homolog B, the group of 7BS DNA/RNA methyltransferases

Gene summary

This gene encodes a homolog of the TRM2 gene in S. cerevisiae. The yeast gene encodes a tRNA methyltransferase that plays a role in tRNA maturation. The yeast protein also has endo-exonuclease activity and may be involved in DNA double strand break repair. Alternative splicing results in multiple transcripts encoding different isoforms. [provided by RefSeq, Nov 2009]

Previous symbols:

CXorf34

MANE transcript

NM_024917.6

Inheritance

—

ClinVar variants

U:154B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chrX:101,009,346-101,052,116

External References & Databases

Ensembl (ENSG00000188917)

Transcript & Mutation Effects

hg38 • Region Span ~42.8 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 TRMT2B variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 37

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024917.6. 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			23 clinvar			23
missense			104 clinvar	4 clinvar		108
nonsense			5 clinvar			5
start loss			2 clinvar			2
frameshift						0
splice donor/acceptor (+/-2bp)			20 clinvar			20
Total	0	0	154	4	0	158

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 63 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024917.6	RefSeq	NP_079193.2	12	MANE Select
ENST00000372936.4	Ensembl	ENSP00000362027.3	12	MANE Select
NM_001167970.2	RefSeq	NP_001161442.1	12	Standard
NM_001167971.2	RefSeq	NP_001161443.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

RNA methylation
tRNA processing

Molecular Function

protein binding
S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372936
Coding exons: 12
Length: 42771
Individuals with no LoFs: 125665
Homozygous LoFs: 11
Heterozygous LoFs: 42
Defined: 125718
p: 0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.03	151	191	0.790	0.0000142	3273
Missense (PolyPhen)		34	38.811	0.87605		735
Synonymous	-0.188	71	69.0	1.03	0.00000491	1016
Loss of Function	1.50	13	20.3	0.641	0.00000163	308

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0023	0.0018	notable
Latino/Admixed American	0.00015	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00016	rare
Finnish	0.00025	0.00018	rare
European (Non-Finnish)	0.00012	0.000088	rare
South Asian	0.000052	0.000033	rare
Other	0.00022	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable S-adenosyl-L-methionine-dependent methyltransferase that catalyzes the formation of 5-methyl-uridine at position 54 (m5U54) in all tRNA. May also have a role in tRNA stabilization or maturation (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.118

Intolerance Scores

LoFtool: 0.925
RVIS EVS: -0.27
RVIS percentile EVS: 34.32

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0351

Gene Damage Prediction

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