EIF4EBP3
Basic information
Region (hg38): 5:140547662-140549576
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
| missense | 5 | |||||
| nonsense | 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) | ||
| 5-140548907-C-A | not specified | Uncertain significance (Feb 28, 2024) | ||
| 5-140548919-C-G | EBV-positive nodal T- and NK-cell lymphoma | Likely benign (-) | ||
| 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) | ||
| 5-140549239-G-A | not specified | Uncertain significance (May 16, 2024) |
GnomAD
Source:
| 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:
- 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
| 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