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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 24.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_032025.5	NP_114414.2	14	yes	-
ENST00000460851.6	ENSP00000417229.1	14	yes	-
NM_001319043.2	NP_001305972.1	13	-	-
NM_001319044.2	NP_001305973.1	12	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• not_specified (62 variants)
• EIF2A-related_disorder (1 variants)
• Dystonia_33 (1 variants)
• Marinesco-Sj�gren_syndrome (1 variants)

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. These statistics are base on transcript: NM_032025.5. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1			1
missense			69	2		71
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3			3
Total	0	0	73	2	0

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
		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

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

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