EIF2A
Basic information
Region (hg38): 3:150546678-150586016
Links
Phenotypes
GenCC
Source:
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 EIF2A 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 | 29 | 31 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 29 | 2 | 0 |
Variants in EIF2A
This is a list of pathogenic ClinVar variants found in the EIF2A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
3-150546806-G-A | not specified | Uncertain significance (Jan 22, 2024) | ||
3-150546818-C-G | not specified | Uncertain significance (Nov 21, 2022) | ||
3-150552359-G-A | not specified | Uncertain significance (May 05, 2023) | ||
3-150558461-A-G | not specified | Uncertain significance (Jan 16, 2024) | ||
3-150562603-G-A | not specified | Uncertain significance (Oct 29, 2021) | ||
3-150563565-A-G | not specified | Uncertain significance (Oct 12, 2022) | ||
3-150563596-A-G | not specified | Uncertain significance (Feb 05, 2024) | ||
3-150564299-G-T | not specified | Uncertain significance (Apr 12, 2022) | ||
3-150564312-T-G | not specified | Uncertain significance (May 25, 2022) | ||
3-150564367-A-G | not specified | Uncertain significance (Dec 28, 2022) | ||
3-150567762-A-C | not specified | Uncertain significance (Mar 29, 2022) | ||
3-150568002-G-T | Dystonia 33 | Uncertain significance (Sep 22, 2024) | ||
3-150568006-C-A | not specified | Uncertain significance (Jun 04, 2024) | ||
3-150568193-A-G | not specified | Uncertain significance (Mar 23, 2023) | ||
3-150568213-C-A | not specified | Uncertain significance (Aug 26, 2022) | ||
3-150571970-C-A | EIF2A-related disorder | Likely benign (Mar 10, 2023) | ||
3-150572021-A-G | not specified | Uncertain significance (Jan 05, 2022) | ||
3-150572054-A-G | not specified | Uncertain significance (Jan 16, 2024) | ||
3-150572075-T-C | not specified | Uncertain significance (Oct 14, 2021) | ||
3-150572093-C-G | not specified | Uncertain significance (Feb 21, 2024) | ||
3-150572129-T-C | not specified | Uncertain significance (Dec 15, 2022) | ||
3-150572246-C-T | not specified | Uncertain significance (May 05, 2023) | ||
3-150572291-G-A | not specified | Uncertain significance (Aug 30, 2022) | ||
3-150572321-A-T | not specified | Uncertain significance (May 28, 2024) | ||
3-150572342-A-C | not specified | Uncertain significance (Mar 06, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
EIF2A | protein_coding | protein_coding | ENST00000460851 | 14 | 37565 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
6.04e-9 | 0.964 | 124577 | 0 | 61 | 124638 | 0.000245 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.10 | 229 | 281 | 0.816 | 0.0000132 | 3805 |
Missense in Polyphen | 62 | 88.052 | 0.70413 | 1235 | ||
Synonymous | 1.31 | 85 | 102 | 0.835 | 0.00000497 | 1089 |
Loss of Function | 2.09 | 18 | 30.4 | 0.592 | 0.00000155 | 410 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000424 | 0.000422 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000279 | 0.000278 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000207 | 0.000204 |
Middle Eastern | 0.000279 | 0.000278 |
South Asian | 0.000594 | 0.000588 |
Other | 0.000506 | 0.000496 |
dbNSFP
Source:
- Function
- FUNCTION: Functions in the early steps of protein synthesis of a small number of specific mRNAs. Acts by directing the binding of methionyl-tRNAi to 40S ribosomal subunits. In contrast to the eIF- 2 complex, it binds methionyl-tRNAi to 40S subunits in a codon- dependent manner, whereas the eIF-2 complex binds methionyl-tRNAi to 40S subunits in a GTP-dependent manner. {ECO:0000269|PubMed:12133843}.;
- Pathway
- Photodynamic therapy-induced unfolded protein response;VEGFA-VEGFR2 Signaling Pathway;Signaling events mediated by TCPTP;IL6;Ceramide signaling pathway;TGF-beta receptor signaling
(Consensus)
Recessive Scores
- pRec
- 0.112
Intolerance Scores
- loftool
- 0.884
- rvis_EVS
- -0.2
- rvis_percentile_EVS
- 38.82
Haploinsufficiency Scores
- pHI
- 0.769
- hipred
- Y
- hipred_score
- 0.661
- ghis
- 0.588
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.560
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Eif2a
- Phenotype
- normal phenotype;
Gene ontology
- Biological process
- translational initiation;regulation of translation;protein phosphorylation;positive regulation of signal transduction;SREBP signaling pathway;ribosome assembly;response to amino acid starvation
- Cellular component
- extracellular space;cytoplasm;eukaryotic translation initiation factor 2 complex;cytosolic small ribosomal subunit;blood microparticle
- Molecular function
- tRNA binding;translation initiation factor activity;protein binding;ribosome binding;cadherin binding