METTL9

methyltransferase like 9, the group of 7BS protein methyltransferases

Basic information

Region (hg38): 16:21597217-21657471

Links

ENSG00000197006 ∙ NCBI:51108 ∙ OMIM:609388 ∙ HGNC:24586 ∙ Uniprot:Q9H1A3 ∙ 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 METTL9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the METTL9 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			16	2		18
Total	0	0	22	2	0

Variants in METTL9

This is a list of pathogenic ClinVar variants found in the METTL9 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-21599740-C-G		not specified	Uncertain significance (Mar 03, 2022)
16-21599746-G-C		not specified	Uncertain significance (Feb 10, 2022)
16-21599767-C-G		not specified	Uncertain significance (Jun 22, 2024)
16-21599771-C-T		not specified	Uncertain significance (Sep 25, 2023)
16-21599854-G-A		not specified	Uncertain significance (Feb 28, 2023)
16-21612649-A-T		not specified	Uncertain significance (Sep 16, 2021)
16-21641543-T-A		not specified	Uncertain significance (Apr 20, 2024)
16-21641562-C-A		not specified	Uncertain significance (Dec 06, 2022)
16-21643105-T-C		not specified	Uncertain significance (Jun 02, 2023)
16-21643138-C-T		not specified	Uncertain significance (May 09, 2022)
16-21643152-C-G		not specified	Uncertain significance (Jan 03, 2024)
16-21643583-G-T		not specified	Uncertain significance (Oct 27, 2023)
16-21643585-G-A		not specified	Uncertain significance (May 17, 2023)
16-21644292-T-C		not specified	Uncertain significance (Nov 22, 2023)
16-21644313-C-T		not specified	Uncertain significance (Nov 09, 2023)
16-21644327-A-G		not specified	Uncertain significance (Sep 14, 2022)
16-21644354-G-A		not specified	Uncertain significance (Apr 26, 2024)
16-21647168-T-C		not specified	Uncertain significance (Feb 27, 2023)
16-21647297-T-G		not specified	Uncertain significance (Mar 18, 2024)
16-21647346-C-A		not specified	Uncertain significance (Sep 25, 2023)
16-21647417-G-A		not specified	Uncertain significance (Dec 16, 2023)
16-21647445-C-G		not specified	Uncertain significance (May 14, 2024)
16-21647456-G-A		not specified	Uncertain significance (Jul 16, 2021)
16-21647489-G-A		not specified	Uncertain significance (May 15, 2023)
16-21652537-C-T		not specified	Likely benign (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
METTL9	protein_coding	protein_coding	ENST00000358154	5	60256

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.804	0.196	125742	0	2	125744	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.62	65	157	0.413	0.00000751	2056
Missense in Polyphen		6	59.175	0.10139		747
Synonymous	-0.495	67	62.0	1.08	0.00000316	602
Loss of Function	2.99	2	14.1	0.141	5.98e-7	181

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.318
• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.268
• hipred: Y
• hipred_score: 0.574
• ghis: 0.592

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.472

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mettl9

Gene ontology

• Molecular function: protein binding