EIF2A

eukaryotic translation initiation factor 2A, the group of WD repeat domain containing

Basic information

Region (hg38): 3:150546678-150586016

Links

ENSG00000144895NCBI:83939OMIM:609234HGNC:3254Uniprot:Q9BY44AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EIF2A gene.

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
clinvar
2
clinvar
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)3087850
3-150546818-C-G not specified Uncertain significance (Nov 21, 2022)2398814
3-150552359-G-A not specified Uncertain significance (May 05, 2023)2550582
3-150558461-A-G not specified Uncertain significance (Jan 16, 2024)3087847
3-150562603-G-A not specified Uncertain significance (Oct 29, 2021)2359648
3-150563565-A-G not specified Uncertain significance (Oct 12, 2022)2318434
3-150563596-A-G not specified Uncertain significance (Feb 05, 2024)3087848
3-150564299-G-T not specified Uncertain significance (Apr 12, 2022)2222099
3-150564312-T-G not specified Uncertain significance (May 25, 2022)3087849
3-150564367-A-G not specified Uncertain significance (Dec 28, 2022)2351017
3-150567762-A-C not specified Uncertain significance (Mar 29, 2022)2280621
3-150568002-G-T Dystonia 33 Uncertain significance (Sep 22, 2024)3362619
3-150568006-C-A not specified Uncertain significance (Jun 04, 2024)3274935
3-150568193-A-G not specified Uncertain significance (Mar 23, 2023)2528891
3-150568213-C-A not specified Uncertain significance (Aug 26, 2022)2309134
3-150571970-C-A EIF2A-related disorder Likely benign (Mar 10, 2023)3052231
3-150572021-A-G not specified Uncertain significance (Jan 05, 2022)2270207
3-150572054-A-G not specified Uncertain significance (Jan 16, 2024)3087851
3-150572075-T-C not specified Uncertain significance (Oct 14, 2021)3087852
3-150572093-C-G not specified Uncertain significance (Feb 21, 2024)3087853
3-150572129-T-C not specified Uncertain significance (Dec 15, 2022)2335692
3-150572246-C-T not specified Uncertain significance (May 05, 2023)2544753
3-150572291-G-A not specified Uncertain significance (Aug 30, 2022)2309750
3-150572321-A-T not specified Uncertain significance (May 28, 2024)3274933
3-150572342-A-C not specified Uncertain significance (Mar 06, 2023)2494318

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
EIF2Aprotein_codingprotein_codingENST00000460851 1437565
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
6.04e-90.9641245770611246380.000245
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.102292810.8160.00001323805
Missense in Polyphen6288.0520.704131235
Synonymous1.31851020.8350.000004971089
Loss of Function2.091830.40.5920.00000155410

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004240.000422
Ashkenazi Jewish0.000.00
East Asian0.0002790.000278
Finnish0.000.00
European (Non-Finnish)0.0002070.000204
Middle Eastern0.0002790.000278
South Asian0.0005940.000588
Other0.0005060.000496

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

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