METTL2B

protein-coding

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

Gene summary

This gene is a member of a family of methyltransferases that share homology with, but are distinct from, the UbiE family of methyltransferases. Alternatively spliced variants which encode different protein isoforms have been described; however, not all variants have been fully characterized. [provided by RefSeq, Jul 2008]

Previous symbols:

METTL2

MANE transcript

NM_018396.3

Inheritance

—

ClinVar variants

U:55B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr7:128,476,729-128,506,602

External References & Databases

Ensembl (ENSG00000165055)

Transcript & Mutation Effects

hg38 • Region Span ~29.9 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 METTL2B variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 52

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018396.3. 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			53 clinvar			53
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	55	1	0	56

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018396.3	RefSeq	NP_060866.2	9	MANE Select
ENST00000262432.13	Ensembl	ENSP00000262432.9	9	MANE Select
ENST00000419443.1	Ensembl	ENSP00000405144.1	4	Standard
ENST00000480046.5	Ensembl	ENSP00000418402.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

tRNA methylation

Molecular Function

tRNA (cytosine) methyltransferase activity
tRNA (cytosine-3-)-methyltransferase activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000262432
Coding exons: 9
Length: 29874
Individuals with no LoFs: 125578
Homozygous LoFs: 2
Heterozygous LoFs: 168
Defined: 125748
p: 0.000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.103	201	205	0.980	0.0000102	2487
Missense (PolyPhen)		72	80.056	0.89937		909
Synonymous	-0.345	79	75.2	1.05	0.00000384	684
Loss of Function	0.935	16	20.6	0.778	0.00000104	236

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0018	0.0018	notable
Latino/Admixed American	0.00023	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.0025	0.0023	notable
European (Non-Finnish)	0.00051	0.00047	rare
South Asian	0.00073	0.00069	rare
Other	0.0013	0.0011	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable S-adenosyl-L-methionine-dependent methyltransferase that mediates 3-methylcytidine modification of some tRNAs. {ECO:0000269|PubMed:21518805}.;

Recessive Scores

pRec: 0.0930

Intolerance Scores

LoFtool: 0.504
RVIS EVS: -0.14
RVIS percentile EVS: 43.77

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.518

Gene Damage Prediction

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