METTL4

methyltransferase 4, N6-adenosine, the group of 7BS N6-adenosine DNA/RNA methyltransferases

Basic information

Region (hg38): 18:2537525-2571509

Links

ENSG00000101574 ∙ NCBI:64863 ∙ OMIM:619626 ∙ HGNC:24726 ∙ Uniprot:Q8N3J2 ∙ 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 METTL4 gene.

• not_specified (52 variants)
• not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the METTL4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000022840.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			52			52
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)		1				1
Total	0	1	52	0	0

Highest pathogenic variant AF is 0.00006302111

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
METTL4	protein_coding	protein_coding	ENST00000574538	8	33985

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.83e-8	0.906	125677	0	65	125742	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.392	223	240	0.929	0.0000116	3112
Missense in Polyphen		54	64.581	0.83617		836
Synonymous	-0.0732	83	82.2	1.01	0.00000388	872
Loss of Function	1.73	15	24.2	0.620	0.00000134	288

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.000220	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000407	0.000396
Middle Eastern	0.000220	0.000217
South Asian	0.000365	0.000359
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable methyltransferase. {ECO:0000250}.

Intolerance Scores

• loftool: 0.815
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.55

Haploinsufficiency Scores

• pHI: 0.112
• hipred: N
• hipred_score: 0.176
• ghis: 0.473

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.468

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mettl4

Gene ontology

• Biological process: DNA methylation on adenine
• Cellular component: nucleus
• Molecular function: nucleic acid binding;site-specific DNA-methyltransferase (adenine-specific) activity