EIF2S1
eukaryotic translation initiation factor 2 subunit alpha
Basic information
Region (hg38): 14:67360327-67386516
Previous symbols: [ "EIF2" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the EIF2S1 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 | 1 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 1 | 1 |
Variants in EIF2S1
This is a list of pathogenic ClinVar variants found in the EIF2S1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 14-67364780-A-C | not specified | Uncertain significance (Aug 17, 2021) | ||
| 14-67364891-A-G | not specified | Uncertain significance (Mar 25, 2024) | ||
| 14-67380676-A-G | not specified | Uncertain significance (May 31, 2023) | ||
| 14-67380708-G-A | not specified | Uncertain significance (Jul 26, 2021) | ||
| 14-67382523-G-A | not specified | Likely benign (Sep 14, 2023) | ||
| 14-67382525-C-G | not specified | Uncertain significance (Sep 14, 2023) | ||
| 14-67382562-A-G | not specified | Uncertain significance (Jul 11, 2023) | ||
| 14-67383389-A-G | Benign (Jun 22, 2018) | |||
| 14-67383419-G-A | not specified | Uncertain significance (Feb 23, 2023) | ||
| 14-67383426-A-G | not specified | Uncertain significance (Jun 02, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| EIF2S1 | protein_coding | protein_coding | ENST00000256383 | 7 | 26520 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.970 | 0.0297 | 123973 | 0 | 1 | 123974 | 0.00000403 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.86 | 67 | 173 | 0.388 | 0.00000873 | 2081 |
| Missense in Polyphen | 10 | 68.361 | 0.14628 | 778 | ||
| Synonymous | 1.47 | 43 | 57.2 | 0.752 | 0.00000268 | 574 |
| Loss of Function | 3.39 | 1 | 15.3 | 0.0654 | 8.86e-7 | 193 |
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) | 0.00000885 | 0.00000885 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S pre-initiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2- GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.;
- Pathway
- Non-alcoholic fatty liver disease (NAFLD) - Homo sapiens (human);Influenza A - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);RNA transport - Homo sapiens (human);Hepatitis C - Homo sapiens (human);Measles - Homo sapiens (human);Apoptosis - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);Translation Factors;Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;Ebola Virus Pathway on Host;Ebola Virus Pathway on Host;double stranded rna induced gene expression;PERK regulates gene expression;skeletal muscle hypertrophy is regulated via akt-mtor pathway;Formation of the ternary complex, and subsequently, the 43S complex;Translation initiation complex formation;Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S;Unfolded Protein Response (UPR);Recycling of eIF2:GDP;Eukaryotic Translation Initiation;Translation;Metabolism of proteins;Transport of small molecules;regulation of eif2;ABC-family proteins mediated transport;eukaryotic protein translation;Ribosomal scanning and start codon recognition;L13a-mediated translational silencing of Ceruloplasmin expression;GTP hydrolysis and joining of the 60S ribosomal subunit;Cap-dependent Translation Initiation;Validated targets of C-MYC transcriptional activation
(Consensus)
Recessive Scores
- pRec
- 0.493
Intolerance Scores
- loftool
- 0.212
- rvis_EVS
- -0.21
- rvis_percentile_EVS
- 38.28
Haploinsufficiency Scores
- pHI
- 0.890
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.691
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.990
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Eif2s1
- 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- translational initiation;aging;negative regulation of translational initiation in response to stress;stress granule assembly;cellular response to amino acid starvation;cellular response to oxidative stress;cellular response to heat;cellular response to UV;response to endoplasmic reticulum stress;PERK-mediated unfolded protein response;protein autophosphorylation;transmembrane transport;positive regulation of neuron death;negative regulation of guanyl-nucleotide exchange factor activity;response to manganese-induced endoplasmic reticulum stress;positive regulation of type B pancreatic cell apoptotic process
- Cellular component
- nucleus;cytosol;polysome;eukaryotic translation initiation factor 2 complex;eukaryotic translation initiation factor 2B complex;cytoplasmic stress granule;membrane;eukaryotic 48S preinitiation complex;multi-eIF complex;translation initiation ternary complex;synapse;extracellular exosome;glial limiting end-foot
- Molecular function
- RNA binding;translation initiation factor activity;protein binding;ribosome binding