EEF1AKMT2

EEF1A lysine methyltransferase 2, the group of 7BS protein lysine methyltransferases

Basic information

Region (hg38): 10:124748149-124791887

Previous symbols: [ "C10orf138", "METTL10" ]

Links

ENSG00000203791 ∙ NCBI:399818 ∙ OMIM:617794 ∙ HGNC:33787 ∙ Uniprot:Q5JPI9 ∙ 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 EEF1AKMT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EEF1AKMT2 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	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in EEF1AKMT2

This is a list of pathogenic ClinVar variants found in the EEF1AKMT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-124762312-G-A		not specified	Uncertain significance (Apr 01, 2022)
10-124762327-T-G		not specified	Uncertain significance (Nov 18, 2023)
10-124765431-T-C		not specified	Uncertain significance (Apr 01, 2024)
10-124765439-G-A		not specified	Uncertain significance (Sep 25, 2023)
10-124765513-A-C		not specified	Uncertain significance (Aug 02, 2023)
10-124765517-T-C		not specified	Uncertain significance (Oct 12, 2022)
10-124774713-T-C		not specified	Likely benign (Dec 16, 2021)
10-124774740-G-A		not specified	Uncertain significance (Mar 02, 2023)
10-124774772-C-A		not specified	Uncertain significance (Dec 08, 2023)
10-124789134-C-T		not specified	Uncertain significance (Aug 02, 2021)
10-124789137-T-C		not specified	Uncertain significance (Jan 08, 2024)
10-124789145-C-G		not specified	Uncertain significance (Mar 06, 2023)
10-124790276-A-G		not specified	Uncertain significance (Mar 16, 2022)
10-124790333-T-A		not specified	Uncertain significance (Jan 19, 2024)
10-124791745-G-A		not specified	Uncertain significance (Oct 06, 2021)
10-124791749-G-A		not specified	Uncertain significance (Dec 14, 2023)
10-124791778-T-A		not specified	Uncertain significance (Feb 14, 2023)
10-124791817-T-C		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EEF1AKMT2	protein_coding	protein_coding	ENST00000368836	6	43722

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.25e-7	0.478	125712	0	33	125745	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.253	128	136	0.939	0.00000622	1855
Missense in Polyphen		30	39.221	0.7649		528
Synonymous	0.333	50	53.1	0.942	0.00000254	578
Loss of Function	0.826	12	15.5	0.774	8.80e-7	183

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000330	0.000330
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000167	0.000167
Middle Eastern	0.000217	0.000217
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein-lysine methyltransferase that selectively catalyzes the trimethylation of EEF1A at 'Lys-318'. {ECO:0000255|HAMAP-Rule:MF_03188, ECO:0000269|PubMed:25144183}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Protein methylation (Consensus)

Recessive Scores

• pRec: 0.0703

Intolerance Scores

• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.28

Haploinsufficiency Scores

• pHI: 0.0692
• hipred: N
• hipred_score: 0.154
• ghis: 0.485

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Eef1akmt2

Gene ontology

• Biological process: protein methylation;peptidyl-lysine methylation
• Cellular component: nucleus;cytoplasm;cytosol
• Molecular function: methyltransferase activity;protein-lysine N-methyltransferase activity