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.

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.

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			43	8		51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding		3	29	31	7	70
Total	0	3	72	39	7

Variants in EEF2KMT

This is a list of pathogenic ClinVar variants found in the EEF2KMT region.

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

Position	Type	Phenotype	Significance	ClinVar
16-5084445-A-G			Benign (Jul 27, 2018)
16-5084499-C-T			Benign (Sep 05, 2018)
16-5084551-C-T			Likely benign (Mar 25, 2020)
16-5084558-G-A		ALG1-congenital disorder of glycosylation	Benign (Mar 26, 2019)
16-5084598-G-C			Likely benign (Jun 25, 2020)
16-5084732-C-G		ALG1-congenital disorder of glycosylation	Likely benign (Jun 28, 2021)
16-5084732-CT-C		ALG1-congenital disorder of glycosylation	Likely benign (Feb 02, 2024)
16-5084733-T-A		ALG1-congenital disorder of glycosylation	Likely benign (Nov 04, 2023)
16-5084734-C-G		ALG1-congenital disorder of glycosylation	Likely benign (Nov 06, 2023)
16-5084734-C-T		not specified	Likely benign (Apr 04, 2017)
16-5084734-CTTTATTT-C		ALG1-congenital disorder of glycosylation	Likely benign (Nov 25, 2024)
16-5084738-A-T		ALG1-congenital disorder of glycosylation	Likely benign (Jan 23, 2025)
16-5084738-AT-A		ALG1-congenital disorder of glycosylation	Benign (Jun 14, 2022)
16-5084738-A-AT		ALG1-congenital disorder of glycosylation	Benign (Mar 27, 2023)
16-5084739-T-G		ALG1-congenital disorder of glycosylation	Uncertain significance (Aug 23, 2022)
16-5084740-T-G		ALG1-congenital disorder of glycosylation	Likely benign (May 27, 2023)
16-5084741-T-A		ALG1-congenital disorder of glycosylation	Likely benign (Jan 11, 2025)
16-5084746-G-C		ALG1-congenital disorder of glycosylation	Likely benign (Dec 06, 2023)
16-5084747-C-T		ALG1-congenital disorder of glycosylation	Uncertain significance (Oct 13, 2023)
16-5084748-A-G		ALG1-congenital disorder of glycosylation	Likely pathogenic (May 08, 2024)
16-5084751-T-C		ALG1-congenital disorder of glycosylation	Uncertain significance (Jun 17, 2024)
16-5084758-C-T		ALG1-congenital disorder of glycosylation	Likely benign (Apr 12, 2023)
16-5084761-A-C		ALG1-congenital disorder of glycosylation	Likely benign (Dec 24, 2023)
16-5084766-T-G		ALG1-congenital disorder of glycosylation	Likely pathogenic (Mar 05, 2021)
16-5084767-T-C		not specified • ALG1-congenital disorder of glycosylation • ALG1-related disorder	Likely benign (Jan 13, 2025)

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