EEF2

eukaryotic translation elongation factor 2, the group of Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 19:3976056-3985463

Previous symbols: [ "EF2" ]

Links

ENSG00000167658 ∙ NCBI:1938 ∙ OMIM:130610 ∙ HGNC:3214 ∙ Uniprot:P13639 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spinocerebellar ataxia type 26 (Supportive), mode of inheritance: AD
• spinocerebellar ataxia type 26 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spinocerebellar ataxia 26	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	15732118; 23001565

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EEF2 gene.

• not provided (1 variants)
• Spinocerebellar ataxia type 26 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EEF2 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			7	91	37	135
missense	1		122	1		124
nonsense		1				1
start loss						0
frameshift			4			4
inframe indel			2			2
splice donor/acceptor (+/-2bp)			1			1
splice region			9	19	3	31
non coding			8	48	35	91
Total	1	1	144	140	72

Variants in EEF2

This is a list of pathogenic ClinVar variants found in the EEF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-3976255-G-A			Benign (Jun 20, 2021)
19-3976323-T-G			Benign (Jun 09, 2021)
19-3976443-G-A			Benign (May 11, 2021)
19-3976551-C-T		not specified • EEF2-related disorder	Benign (May 04, 2021)
19-3976601-G-A		not specified	Benign (Dec 11, 2023)
19-3976610-G-A			Uncertain significance (May 11, 2022)
19-3976623-C-T		not specified	Likely benign (Feb 16, 2022)
19-3976624-G-A			Uncertain significance (Dec 06, 2022)
19-3976635-G-A		EEF2-related disorder	Benign/Likely benign (May 30, 2023)
19-3976648-C-T		not specified	Uncertain significance (Mar 01, 2024)
19-3976652-T-C		not specified	Uncertain significance (Mar 01, 2024)
19-3976656-G-T			Uncertain significance (Sep 28, 2022)
19-3976668-G-A		not specified • EEF2-related disorder	Likely benign (Dec 14, 2016)
19-3976671-C-A		not specified	Likely benign (Jun 22, 2023)
19-3976671-C-G		not specified	Benign (Jan 21, 2024)
19-3976682-A-C			Uncertain significance (Jun 02, 2021)
19-3976690-A-C			Uncertain significance (Feb 13, 2023)
19-3976699-T-C			Uncertain significance (Nov 30, 2022)
19-3976701-G-A		not specified	Benign (Jul 29, 2023)
19-3976707-C-T		not specified • EEF2-related disorder	Benign (Jan 22, 2024)
19-3976708-G-A		not specified	Uncertain significance (Jan 10, 2022)
19-3976716-G-A		not specified	Benign/Likely benign (Sep 05, 2023)
19-3976741-G-A			Uncertain significance (Dec 31, 2023)
19-3976750-G-A			Likely benign (Apr 24, 2023)
19-3976756-G-A			Uncertain significance (May 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EEF2	protein_coding	protein_coding	ENST00000309311	15	9414

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000534	125639	0	2	125641	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.88	235	560	0.420	0.0000368	5597
Missense in Polyphen		61	255.81	0.23845		2502
Synonymous	-6.67	387	252	1.53	0.0000198	1664
Loss of Function	5.31	2	36.7	0.0545	0.00000182	417

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000883	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post- translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome.
• Disease: DISEASE: Spinocerebellar ataxia 26 (SCA26) [MIM:609306]: A form of spinocerebellar ataxia, a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. {ECO:0000269|PubMed:23001565}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Oxytocin signaling pathway - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Translation Factors;AMP-activated Protein Kinase (AMPK) Signaling;Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;Neutrophil degranulation;Disease;Uptake and function of diphtheria toxin;Translation;Post-translational protein modification;Metabolism of proteins;Uptake and actions of bacterial toxins;Synthesis of diphthamide-EEF2;Gamma carboxylation, hypusine formation and arylsulfatase activation;Infectious disease;Innate Immune System;Immune System;Protein methylation;Peptide chain elongation;Eukaryotic Translation Elongation;mTOR signaling pathway (Consensus)

Recessive Scores

• pRec: 0.506

Intolerance Scores

• loftool: 0.101
• rvis_EVS: -2.28
• rvis_percentile_EVS: 1.24

Haploinsufficiency Scores

• pHI: 0.936
• hipred: Y
• hipred_score: 0.783
• ghis: 0.590

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.963

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Eef2
• Phenotype: embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region phenotype; cellular phenotype

Gene ontology

• Biological process: hematopoietic progenitor cell differentiation;response to ischemia;skeletal muscle contraction;translational elongation;aging;glial cell proliferation;response to estradiol;response to endoplasmic reticulum stress;skeletal muscle cell differentiation;response to hydrogen peroxide;neutrophil degranulation;response to ethanol;positive regulation of translation;response to folic acid;cellular response to brain-derived neurotrophic factor stimulus;positive regulation of cytoplasmic translation
• Cellular component: extracellular region;nucleus;cytoplasm;cytosol;plasma membrane;membrane;aggresome;secretory granule lumen;polysomal ribosome;membrane raft;synapse;extracellular exosome;ficolin-1-rich granule lumen;ribonucleoprotein complex
• Molecular function: p53 binding;RNA binding;translation elongation factor activity;GTPase activity;protein binding;GTP binding;5S rRNA binding;protein kinase binding;ribosome binding;cadherin binding;actin filament binding