EIF2A

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

Basic information

Region (hg38): 3:150546678-150586016

Links

ENSG00000144895 ∙ NCBI:83939 ∙ OMIM:609234 ∙ HGNC:3254 ∙ Uniprot:Q9BY44 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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	2		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: gnomAD

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: 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

	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