METTL25

methyltransferase like 25, the group of 7BS orphan methyltransferases

Basic information

Region (hg38): 12:82358528-82479239

Previous symbols: [ "C12orf26" ]

Links

ENSG00000127720 ∙ NCBI:84190 ∙ ∙ HGNC:26228 ∙ Uniprot:Q8N6Q8 ∙ 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 METTL25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the METTL25 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			40	3		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	3	0

Variants in METTL25

This is a list of pathogenic ClinVar variants found in the METTL25 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-82358570-C-T		not specified	Uncertain significance (Jun 23, 2023)
12-82358581-C-T		not specified	Uncertain significance (May 06, 2022)
12-82358602-C-G		not specified	Uncertain significance (Jan 23, 2024)
12-82358660-C-G		not specified	Uncertain significance (Feb 12, 2024)
12-82358690-A-G		not specified	Uncertain significance (Dec 14, 2021)
12-82358693-C-T		not specified	Uncertain significance (Jul 10, 2023)
12-82358716-G-C		not specified	Uncertain significance (Jan 31, 2024)
12-82358737-G-A		not specified	Uncertain significance (Oct 03, 2022)
12-82358746-G-T		not specified	Uncertain significance (Sep 13, 2023)
12-82358747-C-G		not specified	Uncertain significance (Aug 08, 2022)
12-82358761-G-A		not specified	Uncertain significance (Jul 11, 2022)
12-82358773-G-A			Uncertain significance (-)
12-82386890-C-T		not specified	Uncertain significance (Sep 16, 2021)
12-82386896-A-T		not specified	Uncertain significance (Sep 16, 2021)
12-82386957-C-G		not specified	Likely benign (May 08, 2024)
12-82389816-G-A		not specified	Likely benign (Sep 06, 2022)
12-82389825-A-G		not specified	Uncertain significance (Jun 03, 2024)
12-82389836-G-C		not specified	Uncertain significance (Dec 15, 2022)
12-82389884-C-A		not specified	Uncertain significance (Apr 04, 2023)
12-82389909-A-G		not specified	Likely benign (Nov 20, 2023)
12-82398813-G-A		not specified	Uncertain significance (Feb 03, 2023)
12-82398850-A-G		not specified	Uncertain significance (Oct 16, 2023)
12-82398861-G-T		not specified	Uncertain significance (Dec 01, 2022)
12-82398877-C-T		not specified	Uncertain significance (Aug 22, 2023)
12-82399104-T-A		not specified	Uncertain significance (Apr 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
METTL25	protein_coding	protein_coding	ENST00000248306	12	120740

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.19e-13	0.444	125656	0	92	125748	0.000366

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.19	367	308	1.19	0.0000147	3918
Missense in Polyphen		121	111.69	1.0834		1442
Synonymous	-1.58	132	111	1.19	0.00000519	1132
Loss of Function	1.34	23	31.0	0.741	0.00000159	404

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000784	0.000772
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000499	0.000489
Finnish	0.000788	0.000786
European (Non-Finnish)	0.000215	0.000211
Middle Eastern	0.000499	0.000489
South Asian	0.000781	0.000719
Other	0.000508	0.000489

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.71

Haploinsufficiency Scores

• pHI: 0.156
• hipred: N
• hipred_score: 0.206
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mettl25

Gene ontology

• Biological process: methylation
• Molecular function: methyltransferase activity