METTL22

methyltransferase 22, Kin17 lysine, the group of 7BS protein lysine methyltransferases

Basic information

Region (hg38): 16:8621683-8649654

Previous symbols: [ "C16orf68" ]

Links

ENSG00000067365 ∙ NCBI:79091 ∙ OMIM:615261 ∙ HGNC:28368 ∙ Uniprot:Q9BUU2 ∙ 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 METTL22 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the METTL22 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			30	3		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				2		2
Total	0	0	30	6	0

Variants in METTL22

This is a list of pathogenic ClinVar variants found in the METTL22 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-8625685-C-T		not specified	Uncertain significance (Jun 07, 2024)
16-8625686-G-A			Likely benign (Jun 01, 2022)
16-8625723-G-A		not specified	Uncertain significance (May 26, 2024)
16-8625742-T-A		not specified	Uncertain significance (Dec 22, 2023)
16-8625775-G-A		not specified	Uncertain significance (Dec 15, 2023)
16-8628796-G-T		not specified	Uncertain significance (Apr 23, 2024)
16-8628900-G-A		not specified	Uncertain significance (Apr 11, 2023)
16-8628915-A-C		not specified	Uncertain significance (Feb 15, 2023)
16-8628925-A-T		not specified	Uncertain significance (Dec 20, 2023)
16-8628928-T-C		not specified	Likely benign (May 26, 2023)
16-8628966-G-A		not specified	Uncertain significance (Mar 28, 2024)
16-8628976-G-C		not specified	Uncertain significance (Dec 03, 2021)
16-8629025-G-T		not specified	Uncertain significance (Jun 06, 2023)
16-8629035-A-G		not specified	Uncertain significance (May 04, 2022)
16-8629059-G-A		not specified	Uncertain significance (Jan 31, 2022)
16-8629088-C-G		not specified	Uncertain significance (Dec 20, 2023)
16-8635180-G-A		not specified	Uncertain significance (Dec 21, 2023)
16-8635211-G-A		not specified	Likely benign (Sep 13, 2023)
16-8635228-G-C		not specified	Uncertain significance (May 28, 2024)
16-8635259-C-T		not specified	Uncertain significance (Sep 12, 2023)
16-8635295-G-A		not specified	Likely benign (Mar 17, 2023)
16-8635297-A-G		not specified	Uncertain significance (Oct 27, 2022)
16-8639124-G-A		not specified	Uncertain significance (Oct 25, 2023)
16-8639135-C-T		not specified	Uncertain significance (Jul 27, 2022)
16-8639147-C-G		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
METTL22	protein_coding	protein_coding	ENST00000381920	10	24542

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.29e-14	0.0337	124649	1	159	124809	0.000641

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.98	331	244	1.36	0.0000148	2612
Missense in Polyphen		113	84.086	1.3439		951
Synonymous	-1.15	123	108	1.14	0.00000785	817
Loss of Function	0.261	21	22.3	0.940	0.00000140	214

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00108	0.00108
Ashkenazi Jewish	0.00	0.00
East Asian	0.00129	0.00128
Finnish	0.000798	0.000789
European (Non-Finnish)	0.000597	0.000592
Middle Eastern	0.00129	0.00128
South Asian	0.000684	0.000621
Other	0.000333	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein N-lysine methyltransferase. In vitro methylates KIN. {ECO:0000269|PubMed:23349634}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Protein methylation (Consensus)

Intolerance Scores

• rvis_EVS: 0.58
• rvis_percentile_EVS: 82.3

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.204
• ghis: 0.459

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: Mettl22

Zebrafish Information Network

• Gene name: mettl22
• Affected structure: hematopoietic stem cell differentiation
• Phenotype tag: abnormal
• Phenotype quality: disrupted

Gene ontology

• Biological process: protein methylation;peptidyl-lysine methylation
• Cellular component: nucleus;nucleoplasm;nucleolus;protein-containing complex
• Molecular function: protein binding;protein methyltransferase activity;protein-lysine N-methyltransferase activity;heat shock protein binding