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
Phenotypes
GenCC
Source:
- spinocerebellar ataxia type 26 (Supportive), mode of inheritance: AD
- spinocerebellar ataxia type 26 (Strong), mode of inheritance: AD
- neurodevelopmental disorder (Limited), mode of inheritance: AD
- neurodevelopmental disorder (Moderate), mode of inheritance: AD
Clinical Genomic Database
Source:
| 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
- not_provided (396 variants)
- not_specified (137 variants)
- EEF2-related_disorder (15 variants)
- Spinocerebellar_ataxia_type_26 (11 variants)
- Motor_delay (1 variants)
- Spinocerebellar_ataxia_type_19/22 (1 variants)
- EEF2-related_neurodevelopmental_disorder_with_multiple_anomalies (1 variants)
- EEF2-related_Neurodevelopmental_disorder (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. These statistics are base on transcript: NM_000001961.4. 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 10 | 116 | 35 | 161 | ||
| missense | 189 | 194 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 7 | |||||
| splice donor/acceptor (+/-2bp) | 3 | |||||
| Total | 2 | 3 | 208 | 118 | 35 |
Highest pathogenic variant AF is 0.00000137154
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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