METTL15

methyltransferase like 15, the group of 7BS DNA/RNA methyltransferases

Basic information

Region (hg38): 11:28108248-28527041

Previous symbols: [ "METT5D1" ]

Links

ENSG00000169519 ∙ NCBI:196074 ∙ OMIM:618711 ∙ HGNC:26606 ∙ Uniprot:A6NJ78 ∙ 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 METTL15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the METTL15 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			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	2	0

Variants in METTL15

This is a list of pathogenic ClinVar variants found in the METTL15 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-28113341-C-T		not specified	Uncertain significance (Mar 22, 2023)
11-28113366-A-G		not specified	Uncertain significance (May 30, 2024)
11-28113392-G-A		not specified	Uncertain significance (Dec 20, 2023)
11-28113422-C-G		not specified	Uncertain significance (Nov 20, 2023)
11-28113453-A-G		not specified	Uncertain significance (Dec 14, 2021)
11-28113470-C-T		not specified	Uncertain significance (Jan 23, 2024)
11-28113519-A-G		not specified	Uncertain significance (May 05, 2023)
11-28113531-A-G		not specified	Uncertain significance (Dec 28, 2022)
11-28211107-A-G		not specified	Uncertain significance (Oct 03, 2022)
11-28211137-T-C		not specified	Uncertain significance (May 29, 2024)
11-28211194-T-C		not specified	Uncertain significance (Mar 01, 2023)
11-28290222-A-G		not specified	Likely benign (Nov 18, 2022)
11-28290249-G-A		not specified	Uncertain significance (Jul 13, 2021)
11-28290292-G-T		not specified	Uncertain significance (Apr 25, 2023)
11-28290336-C-G		not specified	Uncertain significance (Nov 17, 2023)
11-28296772-G-A		not specified	Uncertain significance (Aug 10, 2021)
11-28296832-G-A		not specified	Uncertain significance (Dec 21, 2022)
11-28296905-C-T		not specified	Uncertain significance (Jul 12, 2022)
11-28330420-A-T		not specified	Uncertain significance (Jun 22, 2023)
11-28330425-C-T		not specified	Uncertain significance (Sep 19, 2022)
11-28330426-G-T		not specified	Uncertain significance (Mar 14, 2023)
11-28330483-G-A		not specified	Uncertain significance (Nov 08, 2022)
11-28330487-A-G		not specified	Uncertain significance (Jan 30, 2024)
11-28330525-T-C		not specified	Uncertain significance (Mar 06, 2023)
11-28330554-G-C		not specified	Uncertain significance (Mar 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
METTL15	protein_coding	protein_coding	ENST00000407364	5	225260

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.78e-10	0.155	125718	0	24	125742	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.241	235	225	1.05	0.0000118	2647
Missense in Polyphen		70	76.233	0.91824		906
Synonymous	-0.594	84	77.4	1.09	0.00000398	788
Loss of Function	0.488	16	18.3	0.877	0.00000102	221

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000213	0.000212
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.000116	0.000114
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable S-adenosyl-L-methionine-dependent methyltransferase. {ECO:0000250}.

Intolerance Scores

• rvis_EVS: -0.12
• rvis_percentile_EVS: 45.13

Haploinsufficiency Scores

• pHI: 0.0958
• hipred: N
• hipred_score: 0.204
• ghis: 0.602

Essentials

• essential_gene_CRISPR: 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: Mettl15

Gene ontology

• Biological process: rRNA base methylation
• Molecular function: rRNA (cytosine-N4-)-methyltransferase activity