EIF4EBP3

eukaryotic translation initiation factor 4E binding protein 3

Basic information

Region (hg38): 5:140547661-140549576

Links

ENSG00000243056 ∙ NCBI:8637 ∙ OMIM:603483 ∙ HGNC:3290 ∙ Uniprot:O60516 ∙ 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 EIF4EBP3 gene.

• Inborn genetic diseases (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EIF4EBP3 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			3			3
missense			4	1		5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in EIF4EBP3

This is a list of pathogenic ClinVar variants found in the EIF4EBP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-140547801-A-C		not specified	Uncertain significance (Apr 13, 2022)
5-140548907-C-A		not specified	Uncertain significance (Feb 28, 2024)
5-140548926-C-T		not specified	Uncertain significance (Jan 04, 2024)
5-140548927-G-A		not specified	Uncertain significance (Aug 10, 2021)
5-140548928-A-C		not specified	Uncertain significance (Jan 20, 2023)
5-140548997-C-T		not specified	Uncertain significance (Dec 05, 2022)
5-140548999-G-A		not specified	Uncertain significance (Jul 14, 2021)
5-140549026-T-C		not specified	Likely benign (Feb 13, 2023)
5-140549053-A-T		not specified	Uncertain significance (Sep 30, 2021)
5-140549057-G-A		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EIF4EBP3	protein_coding	protein_coding	ENST00000310331	3	1913

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000344	0.389	124435	1	90	124526	0.000365

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0940	52	53.9	0.964	0.00000291	628
Missense in Polyphen		15	19.459	0.77087		239
Synonymous	0.394	19	21.3	0.892	0.00000104	209
Loss of Function	-0.0857	5	4.80	1.04	2.89e-7	54

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000489	0.000366
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.00117	0.000611
Middle Eastern	0.000109	0.000109
South Asian	0.000490	0.000392
Other	0.000327	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Repressor of translation initiation that regulates EIF4E activity by preventing its assembly into the eIF4F complex: hypophosphorylated form competes with EIF4G1/EIF4G3 and strongly binds to EIF4E, leading to repress translation. In contrast, hyperphosphorylated form dissociates from EIF4E, allowing interaction between EIF4G1/EIF4G3 and EIF4E, leading to initiation of translation. {ECO:0000250|UniProtKB:Q13541}.
• Pathway: RNA transport - Homo sapiens (human);Translation Factors (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.706
• ghis: 0.449

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.557

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Eif4ebp3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: negative regulation of translational initiation
• Cellular component: cytoplasm;membrane;eukaryotic translation initiation factor 4F complex
• Molecular function: protein binding;eukaryotic initiation factor 4E binding;translation repressor activity