METTL21C

methyltransferase 21C, AARS1 lysine, the group of 7BS protein lysine methyltransferases

Basic information

Region (hg38): 13:102685746-102695044

Previous symbols: [ "C13orf39" ]

Links

ENSG00000139780 ∙ NCBI:196541 ∙ OMIM:615259 ∙ HGNC:33717 ∙ Uniprot:Q5VZV1 ∙ 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 METTL21C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the METTL21C 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			16	4		20
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	5	0

Variants in METTL21C

This is a list of pathogenic ClinVar variants found in the METTL21C region.

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

Position	Type	Phenotype	Significance	ClinVar
13-102686039-A-G		not specified	Uncertain significance (Jun 28, 2023)
13-102686044-A-C		not specified	Uncertain significance (Jun 22, 2021)
13-102686047-A-G		not specified	Likely benign (Dec 15, 2022)
13-102686054-T-TA			Likely benign (Jun 26, 2017)
13-102686072-A-G		not specified	Uncertain significance (Sep 20, 2023)
13-102686138-C-T		not specified	Uncertain significance (Jun 11, 2024)
13-102686144-T-C		not specified	Uncertain significance (Nov 09, 2021)
13-102686191-A-G		not specified	Uncertain significance (Nov 13, 2023)
13-102686240-C-T		not specified	Uncertain significance (Dec 16, 2023)
13-102686976-C-T		not specified	Uncertain significance (Jul 20, 2021)
13-102686981-C-T		not specified	Uncertain significance (Aug 22, 2023)
13-102687013-C-G		not specified	Uncertain significance (Aug 02, 2021)
13-102687021-C-T		not specified	Uncertain significance (Apr 24, 2023)
13-102687024-C-T		not specified	Likely benign (Dec 19, 2023)
13-102690833-C-T		not specified	Uncertain significance (Jun 24, 2022)
13-102690905-C-T		not specified	Uncertain significance (Sep 16, 2021)
13-102694384-C-T		not specified	Uncertain significance (May 08, 2023)
13-102694411-T-C		not specified	Likely benign (Mar 27, 2023)
13-102694437-G-A		not specified	Uncertain significance (Mar 31, 2024)
13-102694443-C-T		not specified	Uncertain significance (Dec 05, 2022)
13-102694458-C-T		not specified	Likely benign (Mar 27, 2023)
13-102694461-C-T		not specified	Uncertain significance (Oct 26, 2021)
13-102694476-G-C		not specified	Uncertain significance (Oct 22, 2021)
13-102694486-G-T		not specified	Uncertain significance (May 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
METTL21C	protein_coding	protein_coding	ENST00000267273	4	8761

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000106	0.351	125630	0	118	125748	0.000469

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0760	145	142	1.02	0.00000738	1701
Missense in Polyphen		56	56.034	0.9994		693
Synonymous	-0.255	62	59.5	1.04	0.00000357	511
Loss of Function	0.452	10	11.7	0.857	4.93e-7	144

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00137	0.00137
Ashkenazi Jewish	0.00	0.00
East Asian	0.00180	0.00180
Finnish	0.00	0.00
European (Non-Finnish)	0.000281	0.000264
Middle Eastern	0.00180	0.00180
South Asian	0.000264	0.000261
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein-lysine methyltransferase. {ECO:0000269|PubMed:22948820}.

Intolerance Scores

• rvis_EVS: 0.93
• rvis_percentile_EVS: 89.7

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.144

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: Mettl21c

Gene ontology

• Biological process: protein methylation;skeletal muscle tissue development;hormone-mediated apoptotic signaling pathway;regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum;peptidyl-lysine methylation;cellular response to dexamethasone stimulus
• Cellular component: nucleus;protein-containing complex
• Molecular function: protein binding;protein-lysine N-methyltransferase activity;heat shock protein binding