EEF2KMT

eukaryotic elongation factor 2 lysine methyltransferase, the group of 7BS protein lysine methyltransferases

Basic information

Region (hg38): 16:5084284-5097795

Previous symbols: [ "FAM86A" ]

Links

ENSG00000118894 ∙ NCBI:196483 ∙ OMIM:615263 ∙ HGNC:32221 ∙ Uniprot:Q96G04 ∙ 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 EEF2KMT gene.

• not_specified (70 variants)
• not_provided (2 variants)
• ALG1-congenital_disorder_of_glycosylation (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EEF2KMT gene is commonly pathogenic or not. These statistics are base on transcript: NM_000201400.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			63	8		71
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	63	8	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EEF2KMT	protein_coding	protein_coding	ENST00000427587	8	13505

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.19e-15	0.00225	125439	1	151	125591	0.000605

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.92	274	198	1.38	0.0000133	2078
Missense in Polyphen		34	29.588	1.1491		408
Synonymous	-2.40	117	88.3	1.33	0.00000628	678
Loss of Function	-0.981	20	15.8	1.27	7.62e-7	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00117	0.00114
Ashkenazi Jewish	0.000398	0.000397
East Asian	0.00104	0.00103
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000552	0.000547
Middle Eastern	0.00104	0.00103
South Asian	0.00128	0.00124
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the trimethylation of eukaryotic elongation factor 2 (EEF2) on 'Lys-525'. {ECO:0000269|PubMed:25231979}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Protein methylation (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• rvis_EVS: 1.62
• rvis_percentile_EVS: 96.01

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.409

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Eef2kmt

Gene ontology

• Biological process: protein methylation;peptidyl-lysine trimethylation
• Cellular component: cytoplasm;cytosol;protein-containing complex
• Molecular function: protein binding;protein-lysine N-methyltransferase activity