METTL25B

protein-coding

methyltransferase like 25B, the group of 7BS orphan methyltransferases

Gene summary

Predicted to enable rRNA (adenine-N6,N6-)-dimethyltransferase activity. Predicted to be involved in rRNA methylation. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C1orf66
RRNAD1

MANE transcript

NM_015997.4

Inheritance

—

ClinVar variants

U:82B:13

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.83

Max pathogenic AF

—

Genomic locus

chr1:156,728,442-156,736,960

External References & Databases

Ensembl (ENSG00000143303)

Transcript & Mutation Effects

hg38 • Region Span ~8.5 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 METTL25B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 89

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015997.4. 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				11 clinvar		11
missense			76 clinvar	2 clinvar		78
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	82	13	0	95

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 63 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015997.4	RefSeq	NP_057081.3	8	MANE Select
ENST00000368216.9	Ensembl	ENSP00000357199.4	8	MANE Select
NM_001142560.2	RefSeq	NP_001136032.1	7	Standard
ENST00000368218.8	Ensembl	ENSP00000357201.4	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

rRNA methylation

Molecular Function

rRNA (adenine-N6,N6-)-dimethyltransferase activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368216
Coding exons: 8
Length: 8519
Individuals with no LoFs: 125647
Homozygous LoFs: 1
Heterozygous LoFs: 100
Defined: 125748
p: 0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.386	265	283	0.935	0.0000166	2994
Missense (PolyPhen)		75	80.335	0.93359		833
Synonymous	1.17	102	118	0.863	0.00000635	1066
Loss of Function	0.770	19	23.0	0.827	0.00000131	228

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00038	0.00038	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00092	0.00092	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00031	0.00031	rare
South Asian	0.0011	0.0010	notable
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: -0.2
RVIS percentile EVS: 38.98

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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