EEF2K

eukaryotic elongation factor 2 kinase, the group of Calmodulin dependent protein kinases

Basic information

Region (hg38): 16:22206278-22288738

Links

ENSG00000103319 ∙ NCBI:29904 ∙ OMIM:606968 ∙ HGNC:24615 ∙ Uniprot:O00418 ∙ 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 EEF2K gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EEF2K 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			80	1		81
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	80	1	0

Variants in EEF2K

This is a list of pathogenic ClinVar variants found in the EEF2K region.

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

Position	Type	Phenotype	Significance	ClinVar
16-22225754-C-T		not specified	Uncertain significance (Feb 16, 2023)
16-22225755-G-A		not specified	Uncertain significance (Mar 09, 2025)
16-22225811-G-C		not specified	Uncertain significance (May 03, 2023)
16-22225817-G-A		not specified	Uncertain significance (Jul 13, 2021)
16-22225869-G-C		not specified	Uncertain significance (Mar 07, 2023)
16-22225917-T-C		not specified	Uncertain significance (May 31, 2023)
16-22225925-A-C		not specified	Uncertain significance (Jan 19, 2025)
16-22244645-G-A		not specified	Uncertain significance (Nov 09, 2024)
16-22244664-A-C		not specified	Uncertain significance (Nov 18, 2022)
16-22244674-C-A		not specified	Uncertain significance (Oct 06, 2021)
16-22244715-G-A		not specified	Uncertain significance (Jul 26, 2024)
16-22244721-C-T		not specified	Uncertain significance (Apr 06, 2024)
16-22244724-G-A		not specified	Uncertain significance (Mar 01, 2024)
16-22250660-G-A		not specified	Uncertain significance (May 17, 2023)
16-22251177-C-A		not specified	Uncertain significance (Dec 21, 2023)
16-22251192-G-T		not specified	Uncertain significance (Nov 10, 2024)
16-22251210-C-T		not specified	Uncertain significance (Apr 20, 2024)
16-22251215-C-T		not specified	Uncertain significance (Sep 02, 2024)
16-22251230-G-A		not specified	Uncertain significance (Jul 26, 2022)
16-22251237-G-A		not specified	Uncertain significance (Feb 28, 2024)
16-22251239-G-A		not specified	Uncertain significance (Oct 01, 2024)
16-22251240-A-G		not specified	Uncertain significance (May 23, 2023)
16-22251261-G-A		not specified	Uncertain significance (Sep 26, 2022)
16-22251294-A-G		not specified	Uncertain significance (Feb 26, 2024)
16-22251318-A-G		not specified	Uncertain significance (Apr 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EEF2K	protein_coding	protein_coding	ENST00000263026	17	80952

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.36e-20	0.0532	125477	0	270	125747	0.00107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.613	432	469	0.920	0.0000303	4801
Missense in Polyphen		136	170.38	0.7982		1746
Synonymous	0.326	193	199	0.971	0.0000147	1347
Loss of Function	1.13	34	41.9	0.812	0.00000239	432

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00190	0.00190
Ashkenazi Jewish	0.00199	0.00199
East Asian	0.000330	0.000326
Finnish	0.000370	0.000370
European (Non-Finnish)	0.00143	0.00143
Middle Eastern	0.000330	0.000326
South Asian	0.000492	0.000490
Other	0.00114	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Threonine kinase that regulates protein synthesis by controlling the rate of peptide chain elongation. Upon activation by a variety of upstream kinases including AMPK or TRPM7, phosphorylates the elongation factor EEF2 at a single site, renders it unable to bind ribosomes and thus inactive. In turn, the rate of protein synthesis is reduced. {ECO:0000269|PubMed:14709557, ECO:0000269|PubMed:9144159}.
• Pathway: Oxytocin signaling pathway - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Translation Factors;AMP-activated Protein Kinase (AMPK) Signaling;BDNF-TrkB Signaling;Signal Transduction;mTORC1-mediated signalling;mTOR signalling;mTOR signaling pathway;Signaling mediated by p38-gamma and p38-delta (Consensus)

Recessive Scores

• pRec: 0.174

Intolerance Scores

• loftool: 0.917
• rvis_EVS: -1.48
• rvis_percentile_EVS: 3.7

Haploinsufficiency Scores

• pHI: 0.109
• hipred: Y
• hipred_score: 0.658
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.977

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Eef2k
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); reproductive system phenotype

Gene ontology

• Biological process: response to ischemia;translational elongation;regulation of protein autophosphorylation;cellular response to insulin stimulus;negative regulation of apoptotic process;positive regulation of endocytosis;protein autophosphorylation;positive regulation of synapse assembly;positive regulation of dendritic spine morphogenesis;cellular response to calcium ion;cellular response to cAMP;cellular response to anoxia;cellular response to brain-derived neurotrophic factor stimulus;response to prolactin
• Cellular component: cytoplasm;cytosol;postsynaptic density;dendritic spine
• Molecular function: protein kinase activity;elongation factor-2 kinase activity;calcium ion binding;calmodulin binding;ATP binding;translation factor activity, RNA binding