METTL21A

methyltransferase 21A, HSPA lysine, the group of 7BS protein lysine methyltransferases

Basic information

Region (hg38): 2:207580630-207625928

Previous symbols: [ "FAM119A" ]

Links

ENSG00000144401 ∙ NCBI:151194 ∙ OMIM:615257 ∙ HGNC:30476 ∙ Uniprot:Q8WXB1 ∙ 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 METTL21A gene.

• Inborn genetic diseases (6 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the METTL21A 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					1	1
Total	0	0	6	0	1

Variants in METTL21A

This is a list of pathogenic ClinVar variants found in the METTL21A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-207597017-C-T			Benign (May 03, 2018)
2-207613167-C-T		not specified	Uncertain significance (Jan 30, 2024)
2-207613240-G-C		not specified	Uncertain significance (Dec 28, 2022)
2-207613303-G-A		not specified	Uncertain significance (Feb 03, 2022)
2-207613387-C-G		not specified	Uncertain significance (Feb 28, 2024)
2-207613387-C-T		not specified	Uncertain significance (Aug 02, 2023)
2-207613393-A-C		not specified	Uncertain significance (Dec 01, 2022)
2-207613438-G-A		not specified	Uncertain significance (Mar 20, 2023)
2-207621815-C-G		not specified	Uncertain significance (Aug 02, 2021)
2-207621829-A-T		not specified	Uncertain significance (Mar 11, 2024)
2-207624365-A-C		not specified	Uncertain significance (Dec 08, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
METTL21A	protein_coding	protein_coding	ENST00000411432	3	45298

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000501	0.699	125510	0	238	125748	0.000947

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0422	123	122	1.01	0.00000641	1402
Missense in Polyphen		44	42.569	1.0336		515
Synonymous	0.806	42	49.2	0.854	0.00000275	442
Loss of Function	0.834	6	8.65	0.694	5.18e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00475	0.00475
Ashkenazi Jewish	0.00	0.00
East Asian	0.00304	0.00305
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000757	0.000756
Middle Eastern	0.00304	0.00305
South Asian	0.000100	0.0000980
Other	0.000826	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein-lysine methyltransferase that selectively trimethylates residues in heat shock protein 70 (HSP70) family members. Contributes to the in vivo trimethylation of Lys residues in HSPA1 and HSPA8. In vitro methylates 'Lys-561' in HSPA1, 'Lys- 564' in HSPA2, 'Lys-585' in HSPA5, 'Lys-563' in HSPA6 and 'Lys- 561' in HSPA8. {ECO:0000269|PubMed:22948820, ECO:0000269|PubMed:23349634, ECO:0000269|PubMed:23921388}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Protein methylation (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.2

Haploinsufficiency Scores

• pHI: 0.147
• hipred: N
• hipred_score: 0.398
• ghis: 0.565

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: Mettl21a

Gene ontology

• Biological process: protein methylation;peptidyl-lysine methylation;regulation of ATPase activity
• Cellular component: nucleoplasm;cytoplasm;protein-containing complex
• Molecular function: protein binding;protein methyltransferase activity;protein-lysine N-methyltransferase activity;Hsp70 protein binding;heat shock protein binding;ATPase binding