EIF4G3
protein-codingeukaryotic translation initiation factor 4 gamma 3, the group of MIF4G domain containing proteins|MicroRNA protein coding host genes
Gene summary
The protein encoded by this gene is thought to be part of the eIF4F protein complex, which is involved in mRNA cap recognition and transport of mRNAs to the ribosome. Interestingly, a microRNA (miR-520c-3p) has been found that negatively regulates synthesis of the encoded protein, and this leads to a global decrease in protein translation and cell proliferation. Therefore, this protein is a key component of the anti-tumor activity of miR-520c-3p. [provided by RefSeq, May 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~371.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to EIF4G3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001391906.1. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | 3 | 7 | |||
| missense | 171 | 6 | 177 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 1 | 180 | 9 | 0 | 190 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001378835.1 | 33 | MANE Select | |
| Ensembl | ENSP00000473510.2 | 33 | MANE Select | |
| RefSeq | NP_001185730.1 | 31 | Standard | |
| RefSeq | NP_001185731.1 | 31 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Viral myocarditis - Homo sapiens (human)
- RNA transport - Homo sapiens (human)
- Translation Factors
- internal ribosome entry pathway
- Cytokine Signaling in Immune system
Biological Process
- translational initiation
- regulation of translational initiation
- negative regulation of autophagy
Molecular Function
- RNA cap binding
- RNA binding
- mRNA binding
- translation initiation factor activity
- translation factor activity, RNA binding
Cellular Component
- cytosol
- eukaryotic translation initiation factor 4F complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000602326
- Coding exons
- 31
- Length
- 370415
- Individuals with no LoFs
- 125730
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 16
- Defined
- 125746
- p
- 0.0000636
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.97 | 605 | 848 | 0.713 | 0.0000438 | 10409 |
| Missense (PolyPhen) | 211 | 388.8 | 0.54269 | 4759 | ||
| Synonymous | 0.0494 | 302 | 303 | 0.996 | 0.0000159 | 3089 |
| Loss of Function | 7.95 | 4 | 81.4 | 0.0491 | 0.00000446 | 957 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00080 | 0.00080 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000027 | 0.000026 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Probable component of the protein complex eIF4F, which is involved in the recognition of the mRNA cap, ATP-dependent unwinding of 5'-terminal secondary structure and recruitment of mRNA to the ribosome. Thought to be a functional homolog of EIF4G1. {ECO:0000269|PubMed:9418880}.;
Intolerance Scores
- LoFtool
- 0.282
- RVIS EVS
- 0.3
- RVIS percentile EVS
- 71.7
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.794
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |