METTL2B

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

Basic information

Region (hg38): 7:128476729-128506602

Previous symbols: [ "METTL2" ]

Links

ENSG00000165055 ∙ NCBI:55798 ∙ OMIM:607846 ∙ HGNC:18272 ∙ Uniprot:Q6P1Q9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the METTL2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the METTL2B gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	19	0	1

Variants in METTL2B

This is a list of pathogenic ClinVar variants found in the METTL2B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-128476805-G-A		not specified	Uncertain significance (Mar 15, 2024)
7-128476806-C-A		not specified	Uncertain significance (Mar 15, 2024)
7-128476818-A-G		not specified	Uncertain significance (Nov 12, 2021)
7-128476848-C-T		not specified	Uncertain significance (Mar 07, 2023)
7-128477139-G-T		not specified	Uncertain significance (Jan 19, 2024)
7-128479173-A-G		not specified	Uncertain significance (Aug 19, 2023)
7-128479218-G-A		not specified	Uncertain significance (May 25, 2022)
7-128479223-T-A		not specified	Uncertain significance (May 14, 2024)
7-128479404-A-G		not specified	Uncertain significance (Jun 06, 2023)
7-128480659-G-A		not specified	Uncertain significance (Nov 18, 2022)
7-128480690-C-T		not specified	Uncertain significance (Feb 06, 2024)
7-128488157-T-C		not specified	Uncertain significance (Feb 28, 2023)
7-128493829-G-A		not specified	Uncertain significance (Dec 13, 2021)
7-128498036-G-A		not specified	Likely benign (Sep 29, 2023)
7-128498066-G-C		not specified	Uncertain significance (Sep 14, 2022)
7-128498073-A-G		not specified	Uncertain significance (Oct 03, 2022)
7-128498109-C-T		not specified	Uncertain significance (Apr 06, 2022)
7-128500903-G-A		not specified	Uncertain significance (Apr 27, 2023)
7-128500906-A-G		not specified	Uncertain significance (Mar 26, 2024)
7-128500928-T-C			Benign (Dec 31, 2019)
7-128500929-G-A		not specified	Uncertain significance (May 25, 2022)
7-128501804-T-C		not specified	Uncertain significance (Oct 17, 2023)
7-128501812-C-G		not specified	Uncertain significance (Feb 05, 2024)
7-128501821-C-T		not specified	Uncertain significance (Mar 14, 2023)
7-128501906-G-C		not specified	Uncertain significance (Aug 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
METTL2B	protein_coding	protein_coding	ENST00000262432	9	29874

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.67e-9	0.390	125578	2	168	125748	0.000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.103	201	205	0.980	0.0000102	2487
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00201	0.00201
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00246	0.00227
European (Non-Finnish)	0.000506	0.000466
Middle Eastern	0.000218	0.000217
South Asian	0.000730	0.000686
Other	0.00125	0.00114

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.101
• hipred: Y
• hipred_score: 0.546
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.518

Gene Damage Prediction

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

Gene ontology

• Biological process: tRNA methylation
• Molecular function: tRNA (cytosine) methyltransferase activity;tRNA (cytosine-3-)-methyltransferase activity