EEF1A1
Basic information
Region (hg38): 6:73489308-73525587
Previous symbols: [ "EF1A", "EEF1A", "LENG7" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (12 variants)
- not_provided (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the EEF1A1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001402.6. 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 | 2 | |||||
| missense | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 13 | 0 | 2 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| EEF1A1 | protein_coding | protein_coding | ENST00000316292 | 7 | 8048 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.979 | 0.0214 | 125719 | 0 | 9 | 125728 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.72 | 90 | 258 | 0.348 | 0.0000127 | 3012 |
| Missense in Polyphen | 16 | 67.64 | 0.23655 | 940 | ||
| Synonymous | -5.29 | 156 | 91.6 | 1.70 | 0.00000456 | 921 |
| Loss of Function | 3.50 | 1 | 16.2 | 0.0618 | 7.45e-7 | 211 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000975 | 0.0000905 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000621 | 0.0000615 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis. With PARP1 and TXK, forms a complex that acts as a T helper 1 (Th1) cell-specific transcription factor and binds the promoter of IFN-gamma to directly regulate its transcription, and is thus involved importantly in Th1 cytokine production. {ECO:0000269|PubMed:17177976}.;
- Pathway
- Legionellosis - Homo sapiens (human);RNA transport - Homo sapiens (human);Translation Factors;Neutrophil degranulation;HSF1 activation;west nile virus;Translation;Cellular responses to stress;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;Cellular responses to external stimuli;EGFR1;Cellular response to heat stress;Protein methylation;Peptide chain elongation;Eukaryotic Translation Elongation
(Consensus)
Recessive Scores
- pRec
- 0.696
Intolerance Scores
- loftool
- 0.0919
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 33.97
Haploinsufficiency Scores
- pHI
- 0.988
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.644
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.999
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Eef1a1
- Phenotype
- immune system phenotype; hematopoietic system 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); neoplasm;
Gene ontology
- Biological process
- translation;translational elongation;neutrophil degranulation;cellular response to epidermal growth factor stimulus;regulation of chaperone-mediated autophagy
- Cellular component
- extracellular region;extracellular space;nucleus;nucleolus;cytoplasm;cytosol;eukaryotic translation elongation factor 1 complex;plasma membrane;membrane;cortical actin cytoskeleton;ruffle membrane;secretory granule lumen;extracellular exosome;cytoplasmic side of lysosomal membrane;ficolin-1-rich granule lumen
- Molecular function
- tRNA binding;RNA binding;translation elongation factor activity;GTPase activity;protein binding;GTP binding;protein kinase binding