METTL25B

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

Basic information

Region (hg38): 1:156728442-156736960

Previous symbols: [ "C1orf66", "RRNAD1" ]

Links

ENSG00000143303 ∙ NCBI:51093 ∙ ∙ HGNC:24273 ∙ Uniprot:Q96FB5 ∙ 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 METTL25B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the METTL25B 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			33	1		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	1	0

Variants in METTL25B

This is a list of pathogenic ClinVar variants found in the METTL25B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-156729151-A-G		not specified	Uncertain significance (Jun 06, 2022)
1-156729187-A-G		not specified	Uncertain significance (Oct 20, 2023)
1-156732012-T-C		not specified	Uncertain significance (Jan 26, 2023)
1-156732015-G-C		not specified	Uncertain significance (Feb 27, 2023)
1-156732325-C-T		not specified	Uncertain significance (May 14, 2024)
1-156732406-G-A		not specified	Uncertain significance (Jun 03, 2022)
1-156732423-C-T		not specified	Uncertain significance (Jul 25, 2023)
1-156732424-G-A		not specified	Uncertain significance (Feb 28, 2023)
1-156732426-A-G		not specified	Uncertain significance (Aug 02, 2021)
1-156733004-A-G		not specified	Uncertain significance (Dec 15, 2023)
1-156733033-G-A		not specified	Uncertain significance (Jan 03, 2024)
1-156733415-G-T		not specified	Uncertain significance (Sep 22, 2022)
1-156733452-G-A		not specified	Uncertain significance (Jun 29, 2022)
1-156734028-G-A		not specified	Uncertain significance (May 03, 2023)
1-156734045-G-A		not specified	Uncertain significance (Aug 08, 2022)
1-156734062-C-A		not specified	Uncertain significance (Dec 19, 2022)
1-156734088-T-C		not specified	Uncertain significance (Dec 12, 2023)
1-156734123-C-G		not specified	Uncertain significance (Dec 16, 2021)
1-156734123-C-T		not specified	Uncertain significance (May 11, 2022)
1-156734124-G-A		not specified	Uncertain significance (Feb 27, 2024)
1-156734139-G-A		not specified	Uncertain significance (Aug 08, 2022)
1-156734156-G-A		not specified	Uncertain significance (Jan 09, 2024)
1-156734169-C-G		not specified	Uncertain significance (Aug 02, 2023)
1-156734294-T-C		not specified	Uncertain significance (Jun 29, 2023)
1-156734316-G-A		not specified	Uncertain significance (Aug 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
METTL25B	protein_coding	protein_coding	ENST00000368216	8	8519

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.40e-11	0.188	125647	1	100	125748	0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.386	265	283	0.935	0.0000166	2994
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000566	0.000564
Ashkenazi Jewish	0.00	0.00
East Asian	0.000924	0.000925
Finnish	0.00	0.00
European (Non-Finnish)	0.000311	0.000308
Middle Eastern	0.000924	0.000925
South Asian	0.00109	0.00105
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.98

Haploinsufficiency Scores

• pHI: 0.145
• hipred: N
• hipred_score: 0.244
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rrnad1

Gene ontology

• Biological process: rRNA methylation
• Cellular component: integral component of membrane
• Molecular function: rRNA (adenine-N6,N6-)-dimethyltransferase activity