METTL13

methyltransferase 13, eEF1A lysine and N-terminal methyltransferase, the group of 7BS protein lysine methyltransferases

Basic information

Region (hg38): 1:171781659-171814023

Previous symbols: [ "KIAA0859", "DFNM1", "EEF1AKNMT" ]

Links

ENSG00000010165 ∙ NCBI:51603 ∙ OMIM:617987 ∙ HGNC:24248 ∙ Uniprot:Q8N6R0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, nonsyndromic, modifier 1	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Audiologic/Otolaryngologic	29408807
Heterozygous variants have a protective effect (related to nonsyndromic deafness) for individuals with homozygous pathogenic variants in GAB1

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the METTL13 gene.

• Inborn genetic diseases (35 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the METTL13 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			34	1		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	1	0

Variants in METTL13

This is a list of pathogenic ClinVar variants found in the METTL13 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-171782050-C-A		not specified	Uncertain significance (Oct 17, 2023)
1-171782062-A-G		not specified	Uncertain significance (Sep 26, 2022)
1-171782096-T-C		METTL13-related disorder	Benign (Oct 17, 2019)
1-171783818-G-A		not specified	Uncertain significance (Dec 19, 2023)
1-171783839-A-G		not specified	Uncertain significance (May 05, 2023)
1-171783873-C-A		not specified	Uncertain significance (Feb 28, 2023)
1-171783899-A-G		METTL13-related disorder	Benign (Oct 17, 2019)
1-171783945-A-G		not specified	Uncertain significance (Nov 30, 2021)
1-171783958-G-C		METTL13-related disorder	Likely benign (Jul 30, 2019)
1-171783989-A-T		not specified	Uncertain significance (Jun 21, 2023)
1-171784023-T-C		not specified	Uncertain significance (Mar 01, 2024)
1-171784049-C-T		not specified	Uncertain significance (Dec 01, 2022)
1-171784089-A-G		not specified	Uncertain significance (Sep 17, 2021)
1-171784117-G-T		not specified	Uncertain significance (Dec 03, 2021)
1-171784135-G-A		METTL13-related disorder	Benign (Oct 22, 2019)
1-171784166-T-A		not specified	Uncertain significance (Jan 24, 2024)
1-171784241-G-T		not specified	Uncertain significance (Feb 28, 2023)
1-171784246-T-A		METTL13-related disorder	Likely benign (Jul 24, 2019)
1-171784286-G-A		not specified	Uncertain significance (Jan 26, 2022)
1-171784321-G-A		METTL13-related disorder	Likely benign (May 23, 2019)
1-171784367-C-T		not specified	Uncertain significance (Mar 14, 2023)
1-171784368-G-A		not specified	Uncertain significance (Feb 06, 2024)
1-171784414-C-A		not specified	Uncertain significance (Aug 08, 2023)
1-171784416-C-T		not specified	Uncertain significance (Jul 09, 2021)
1-171784473-G-A		METTL13-related disorder	Benign (Jul 11, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
METTL13	protein_coding	protein_coding	ENST00000361735	8	32376

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.63e-9	0.954	125680	1	67	125748	0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	350	409	0.855	0.0000239	4579
Missense in Polyphen		88	123.15	0.71456		1350
Synonymous	-0.332	169	164	1.03	0.00000902	1398
Loss of Function	2.04	19	31.3	0.606	0.00000192	315

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000606	0.000543
Ashkenazi Jewish	0.00	0.00
East Asian	0.000327	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000390	0.000378
Middle Eastern	0.000327	0.000326
South Asian	0.000151	0.000131
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.102

Intolerance Scores

• rvis_EVS: -0.66
• rvis_percentile_EVS: 15.95

Haploinsufficiency Scores

• pHI: 0.249
• hipred: N
• hipred_score: 0.496
• ghis: 0.636

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Mettl13