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.

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.

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			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region						0
non coding						0
Total	0	1	27	0	0

Variants in METTL4

This is a list of pathogenic ClinVar variants found in the METTL4 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-2539016-A-T		not specified	Uncertain significance (Dec 19, 2023)
18-2539046-T-C		not specified	Uncertain significance (Mar 30, 2024)
18-2544197-G-A		not specified	Uncertain significance (Jun 11, 2021)
18-2544207-G-T		not specified	Uncertain significance (Jun 10, 2024)
18-2544213-G-A		not specified	Uncertain significance (Feb 17, 2024)
18-2544215-G-A		not specified	Uncertain significance (Dec 27, 2023)
18-2544234-C-T		not specified	Uncertain significance (Jun 22, 2021)
18-2544270-C-T		not specified	Uncertain significance (May 30, 2023)
18-2544681-C-A		not specified	Uncertain significance (Mar 03, 2022)
18-2544683-C-T		not specified	Uncertain significance (Oct 05, 2023)
18-2547456-C-G		not specified	Uncertain significance (Oct 26, 2022)
18-2547467-T-C		not specified	Uncertain significance (Mar 06, 2023)
18-2547479-A-G		not specified	Uncertain significance (Dec 05, 2022)
18-2547492-G-C		not specified	Uncertain significance (Oct 27, 2023)
18-2547513-G-A		not specified	Uncertain significance (May 24, 2024)
18-2552702-T-C		not specified	Uncertain significance (Mar 08, 2024)
18-2552762-T-C		not specified	Uncertain significance (Jan 12, 2024)
18-2554668-C-T			Likely pathogenic (Jun 27, 2022)
18-2554671-T-C		not specified	Uncertain significance (Aug 17, 2021)
18-2554725-G-A		not specified	Uncertain significance (Dec 03, 2021)
18-2554759-C-A		not specified	Uncertain significance (Aug 02, 2021)
18-2554773-G-C		not specified	Uncertain significance (Aug 02, 2021)
18-2554791-C-A		not specified	Uncertain significance (May 05, 2023)
18-2554822-T-C		not specified	Uncertain significance (Oct 03, 2023)
18-2554924-G-T		not specified	Uncertain significance (Jan 24, 2024)

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