METTL2A

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

Basic information

Region (hg38): 17:62423875-62453385

Links

ENSG00000087995 ∙ NCBI:339175 ∙ OMIM:618902 ∙ HGNC:25755 ∙ Uniprot:Q96IZ6 ∙ 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 METTL2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the METTL2A 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						0
missense			29	2		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	2	0

Variants in METTL2A

This is a list of pathogenic ClinVar variants found in the METTL2A region.

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

Position	Type	Phenotype	Significance	ClinVar
17-62423910-G-C		not specified	Uncertain significance (Dec 11, 2023)
17-62423919-C-A		not specified	Uncertain significance (Dec 25, 2024)
17-62423942-G-A		not specified	Uncertain significance (Dec 12, 2024)
17-62424297-C-G		not specified	Uncertain significance (Sep 27, 2024)
17-62424298-C-A		not specified	Uncertain significance (Sep 27, 2024)
17-62426332-A-C		not specified	Uncertain significance (Oct 29, 2024)
17-62426479-A-G		not specified	Likely benign (Jan 30, 2024)
17-62426503-T-C		not specified	Likely benign (Aug 21, 2023)
17-62426573-G-C		not specified	Uncertain significance (Jan 02, 2024)
17-62426644-G-A		not specified	Uncertain significance (Feb 19, 2025)
17-62435237-C-A		not specified	Uncertain significance (Dec 18, 2023)
17-62435247-T-G		not specified	Uncertain significance (Feb 08, 2025)
17-62435254-T-G		not specified	Uncertain significance (Apr 20, 2023)
17-62440639-C-T		not specified	Uncertain significance (Jun 29, 2023)
17-62440641-C-G		not specified	Uncertain significance (Nov 24, 2024)
17-62440641-C-T		not specified	Uncertain significance (Jul 10, 2023)
17-62440645-G-C		not specified	Uncertain significance (Jan 16, 2024)
17-62440725-A-G		not specified	Uncertain significance (Apr 06, 2024)
17-62440741-C-T		not specified	Uncertain significance (Oct 12, 2021)
17-62440743-A-T		not specified	Uncertain significance (Mar 29, 2022)
17-62444853-A-G		not specified	Uncertain significance (Oct 29, 2024)
17-62444907-G-A		not specified	Uncertain significance (May 09, 2022)
17-62444931-C-T		not specified	Uncertain significance (Oct 05, 2023)
17-62444932-G-A		not specified	Uncertain significance (Jan 10, 2023)
17-62444939-A-T		not specified	Uncertain significance (Sep 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
METTL2A	protein_coding	protein_coding	ENST00000311506	9	26227

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.76e-13	0.0457	125441	0	307	125748	0.00122

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0738	199	202	0.985	0.0000103	2492
Missense in Polyphen		51	55.66	0.91628		588
Synonymous	0.912	66	76.1	0.867	0.00000407	690
Loss of Function	0.297	20	21.5	0.931	0.00000115	239

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0112	0.0112
Ashkenazi Jewish	0.00	0.00
East Asian	0.000114	0.000109
Finnish	0.000323	0.000323
European (Non-Finnish)	0.000230	0.000229
Middle Eastern	0.000114	0.000109
South Asian	0.000834	0.000817
Other	0.00115	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable S-adenosyl-L-methionine-dependent methyltransferase that mediates 3-methylcytidine modification of some tRNAs. {ECO:0000250}.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.694
• rvis_EVS: 0.19
• rvis_percentile_EVS: 67.03

Haploinsufficiency Scores

• pHI: 0.155
• hipred: N
• hipred_score: 0.187
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.201

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mettl2
• Phenotype: cellular phenotype

Gene ontology

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