METTL25

protein-coding

methyltransferase like 25, the group of 7BS orphan methyltransferases

Gene summary

Predicted to enable methyltransferase activity. Predicted to be involved in methylation. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C12orf26

MANE transcript

NM_032230.3

Inheritance

—

ClinVar variants

U:102B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.74

Max pathogenic AF

—

Genomic locus

chr12:82,358,528-82,479,239

External References & Databases

Ensembl (ENSG00000127720)

Transcript & Mutation Effects

hg38 • Region Span ~120.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to METTL25 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 101

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032230.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense			97 clinvar	10 clinvar		107
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	102	11	0	113

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032230.3	RefSeq	NP_115606.2	12	MANE Select
ENST00000248306.8	Ensembl	ENSP00000248306.3	12	MANE Select
NM_001319675.2	RefSeq	NP_001306604.1	11	Standard
NM_001347934.2	RefSeq	NP_001334863.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

methylation

Molecular Function

methyltransferase activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000248306
Coding exons: 12
Length: 120740
Individuals with no LoFs: 125656
Homozygous LoFs: 0
Heterozygous LoFs: 92
Defined: 125748
p: 0.000366

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.19	367	308	1.19	0.0000147	3918
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00057	0.00055	rare
Latino/Admixed American	0.00022	0.00020	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00050	0.00049	rare
Finnish	0.00079	0.00079	rare
European (Non-Finnish)	0.00022	0.00021	rare
South Asian	0.00078	0.00072	rare
Other	0.00051	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

RVIS EVS: 0.31
RVIS percentile EVS: 72.71

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N

Gene Damage Prediction

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