EEF1AKMT1

EEF1A lysine methyltransferase 1, the group of 7BS protein lysine methyltransferases

Basic information

Region (hg38): 13:20728730-20773961

Previous symbols: [ "N6AMT2" ]

Links

ENSG00000150456 ∙ NCBI:221143 ∙ OMIM:617793 ∙ HGNC:27351 ∙ Uniprot:Q8WVE0 ∙ 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 EEF1AKMT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EEF1AKMT1 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in EEF1AKMT1

This is a list of pathogenic ClinVar variants found in the EEF1AKMT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-20731865-G-A		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EEF1AKMT1	protein_coding	protein_coding	ENST00000382758	4	45228

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000244	0.306	125732	0	15	125747	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.252	112	120	0.935	0.00000639	1413
Missense in Polyphen		52	53.28	0.97598		633
Synonymous	-0.863	55	47.4	1.16	0.00000286	387
Loss of Function	0.249	9	9.84	0.914	4.16e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000155	0.000152
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000723	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein-lysine methyltransferase that selectively catalyzes the trimethylation of EEF1A at 'Lys-79'. {ECO:0000255|HAMAP-Rule:MF_03187, ECO:0000269|PubMed:26545399}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Protein methylation (Consensus)

Recessive Scores

• pRec: 0.0934

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.197
• ghis: 0.521

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Eef1akmt1
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein methylation;peptidyl-lysine methylation
• Cellular component: cytosol
• Molecular function: nucleic acid binding;methyltransferase activity;protein-lysine N-methyltransferase activity