EIF2D

eukaryotic translation initiation factor 2D

Basic information

Region (hg38): 1:206571292-206612465

Links

ENSG00000143486 ∙ NCBI:1939 ∙ OMIM:613709 ∙ HGNC:6583 ∙ Uniprot:P41214 ∙ 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 EIF2D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EIF2D 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		1
missense			41	2		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	41	3	0

Variants in EIF2D

This is a list of pathogenic ClinVar variants found in the EIF2D region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-206583317-G-A		not specified	Uncertain significance (Apr 24, 2024)
1-206583348-C-T		not specified	Uncertain significance (Aug 12, 2024)
1-206583351-G-A		not specified	Uncertain significance (Jul 06, 2021)
1-206584442-C-T		not specified	Uncertain significance (Mar 07, 2025)
1-206584481-A-G		not specified	Uncertain significance (Jul 23, 2024)
1-206584514-C-T		not specified	Uncertain significance (Feb 15, 2023)
1-206584586-C-T		not specified	Uncertain significance (Jul 16, 2024)
1-206584660-A-G		not specified	Uncertain significance (Jan 03, 2022)
1-206584664-G-A		not specified	Uncertain significance (Feb 28, 2024)
1-206584666-A-T		not specified	Uncertain significance (Sep 27, 2022)
1-206584670-A-G		not specified	Uncertain significance (Jul 02, 2024)
1-206585210-G-A		not specified	Uncertain significance (Aug 04, 2023)
1-206585242-G-A		not specified	Uncertain significance (Feb 15, 2023)
1-206585288-A-C		not specified	Uncertain significance (Jan 17, 2024)
1-206586841-A-C		not specified	Uncertain significance (May 01, 2024)
1-206586889-G-C		not specified	Uncertain significance (Jun 02, 2023)
1-206591798-G-A		not specified	Uncertain significance (May 17, 2023)
1-206593622-G-A		not specified	Uncertain significance (May 31, 2023)
1-206593626-T-C		not specified	Likely benign (Nov 11, 2024)
1-206593691-G-A		not specified	Uncertain significance (Jul 06, 2021)
1-206593723-C-T		not specified	Uncertain significance (Aug 02, 2021)
1-206593780-C-T		not specified	Uncertain significance (Aug 02, 2023)
1-206593787-C-T		not specified	Uncertain significance (Aug 01, 2024)
1-206595731-G-A		not specified	Uncertain significance (Oct 22, 2021)
1-206595782-A-G		not specified	Uncertain significance (Mar 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EIF2D	protein_coding	protein_coding	ENST00000271764	15	41285

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.23e-9	0.993	125689	0	59	125748	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	241	318	0.757	0.0000162	3802
Missense in Polyphen		51	97.233	0.52451		1263
Synonymous	1.32	108	127	0.850	0.00000685	1153
Loss of Function	2.53	20	36.5	0.548	0.00000204	387

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000835	0.000834
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000323	0.000323
European (Non-Finnish)	0.000203	0.000202
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Translation initiation factor that is able to deliver tRNA to the P-site of the eukaryotic ribosome in a GTP-independent manner. The binding of Met-tRNA(I) occurs after the AUG codon finds its position in the P-site of 40S ribosomes, the situation that takes place during initiation complex formation on some specific RNAs. Its activity in tRNA binding with 40S subunits does not require the presence of the aminoacyl moiety. Possesses the unique ability to deliver non-Met (elongator) tRNAs into the P- site of the 40S subunit. In addition to its role in initiation, can promote release of deacylated tRNA and mRNA from recycled 40S subunits following ABCE1-mediated dissociation of post-termination ribosomal complexes into subunits. {ECO:0000269|PubMed:20566627, ECO:0000269|PubMed:20713520}.

Recessive Scores

• pRec: 0.134

Intolerance Scores

• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.73

Haploinsufficiency Scores

• pHI: 0.249
• hipred: Y
• hipred_score: 0.506
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Eif2d

Gene ontology

• Biological process: formation of translation preinitiation complex;intracellular protein transport;ribosome disassembly;IRES-dependent viral translational initiation
• Cellular component: cytoplasm;cytosol;nuclear body;cytosolic small ribosomal subunit
• Molecular function: translation initiation factor activity;signaling receptor activity