EIF4EBP3

eukaryotic translation initiation factor 4E binding protein 3

Basic information

Region (hg38): 5:140547662-140549576

Links

ENSG00000243056NCBI:8637OMIM:603483HGNC:3290Uniprot:O60516AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EIF4EBP3 gene.

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
clinvar
3
missense
4
clinvar
1
clinvar
5
nonsense
1
clinvar
1
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
0
Total 0 0 8 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)2388992
5-140548907-C-A not specified Uncertain significance (Feb 28, 2024)3121044
5-140548919-C-G EBV-positive nodal T- and NK-cell lymphoma Likely benign (-)2681256
5-140548926-C-T not specified Uncertain significance (Jan 04, 2024)3121049
5-140548927-G-A not specified Uncertain significance (Aug 10, 2021)2242250
5-140548928-A-C not specified Uncertain significance (Jan 20, 2023)2476991
5-140548997-C-T not specified Uncertain significance (Dec 05, 2022)2224332
5-140548999-G-A not specified Uncertain significance (Jul 14, 2021)2237325
5-140549026-T-C not specified Likely benign (Feb 13, 2023)2483070
5-140549053-A-T not specified Uncertain significance (Sep 30, 2021)2354989
5-140549057-G-A not specified Uncertain significance (Jun 06, 2023)2558174
5-140549239-G-A not specified Uncertain significance (May 16, 2024)3275043

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
EIF4EBP3protein_codingprotein_codingENST00000310331 31913
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0003440.3891244351901245260.000365
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.09405253.90.9640.00000291628
Missense in Polyphen1519.4590.77087239
Synonymous0.3941921.30.8920.00000104209
Loss of Function-0.085754.801.042.89e-754

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004890.000366
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.00009240.0000924
European (Non-Finnish)0.001170.000611
Middle Eastern0.0001090.000109
South Asian0.0004900.000392
Other0.0003270.000163

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

loftool
rvis_EVS
0.01
rvis_percentile_EVS
54.63

Haploinsufficiency Scores

pHI
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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