METTL27

methyltransferase like 27, the group of 7BS orphan methyltransferases

Basic information

Region (hg38): 7:73834590-73842516

Previous symbols: [ "WBSCR27" ]

Links

ENSG00000165171 ∙ NCBI:155368 ∙ OMIM:612546 ∙ HGNC:19068 ∙ Uniprot:Q8N6F8 ∙ 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 METTL27 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the METTL27 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				1		1
missense			14	2		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region						0
non coding						0
Total	0	0	14	4	0

Variants in METTL27

This is a list of pathogenic ClinVar variants found in the METTL27 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-73834775-C-T		not specified	Uncertain significance (Apr 12, 2022)
7-73834795-G-A			Likely benign (Jun 01, 2024)
7-73834842-C-T			Likely benign (Oct 01, 2022)
7-73834862-C-T		not specified	Uncertain significance (Feb 06, 2023)
7-73834863-G-A		not specified	Likely benign (Jun 28, 2024)
7-73834874-G-A		not specified	Uncertain significance (May 10, 2024)
7-73834883-G-T		not specified	Uncertain significance (Sep 26, 2022)
7-73834939-T-G		not specified	Uncertain significance (Jun 30, 2023)
7-73834968-C-T			Likely benign (Oct 01, 2024)
7-73840034-G-T		not specified	Uncertain significance (Aug 02, 2022)
7-73840045-T-C		not specified	Likely benign (Dec 18, 2023)
7-73840108-G-A		not specified	Uncertain significance (May 04, 2022)
7-73840109-C-T		not specified	Uncertain significance (Jan 23, 2024)
7-73840121-C-CTG		not specified	Likely benign (Mar 29, 2016)
7-73840416-T-G		not specified	Uncertain significance (Sep 30, 2024)
7-73840419-G-C		not specified	Uncertain significance (Feb 27, 2023)
7-73840462-G-A		not specified	Uncertain significance (Nov 15, 2021)
7-73840474-C-T		not specified	Uncertain significance (Mar 25, 2024)
7-73840477-G-A		not specified	Uncertain significance (Dec 13, 2023)
7-73840513-C-G		not specified	Uncertain significance (Aug 01, 2024)
7-73840546-G-A		not specified	Uncertain significance (Nov 09, 2024)
7-73841118-A-C		not specified	Uncertain significance (May 14, 2024)
7-73841156-C-T		not specified	Uncertain significance (Feb 13, 2024)
7-73842026-A-G		not specified	Uncertain significance (Dec 15, 2023)
7-73842049-A-C		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
METTL27	protein_coding	protein_coding	ENST00000297873	5	7946

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0598	0.875	124767	50	915	125732	0.00384

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.456	161	146	1.11	0.00000862	1531
Missense in Polyphen		37	30.699	1.2053		379
Synonymous	-0.956	79	68.9	1.15	0.00000461	533
Loss of Function	1.55	3	7.60	0.395	3.25e-7	87

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00511	0.00485
Ashkenazi Jewish	0.0272	0.0217
East Asian	0.00614	0.00441
Finnish	0.00284	0.00222
European (Non-Finnish)	0.00332	0.00289
Middle Eastern	0.00614	0.00441
South Asian	0.00834	0.00544
Other	0.00349	0.00277

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Note=METTL27 is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region. Haploinsufficiency of METTL27 may be the cause of certain cardiovascular and musculo-skeletal abnormalities observed in the disease. {ECO:0000269|Ref.1}.

Intolerance Scores

• rvis_EVS: 1.31
• rvis_percentile_EVS: 94

Haploinsufficiency Scores

• pHI: 0.0641
• hipred: N
• hipred_score: 0.145
• ghis: 0.461

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Mettl27

Gene ontology

• Molecular function: protein binding