EIF3D
eukaryotic translation initiation factor 3 subunit D, the group of Eukaryotic translation initiation factor 3|Armadillo like helical domain containing
Basic information
Region (hg38): 22:36510855-36529184
Previous symbols: [ "EIF3S7" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
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 EIF3D 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 | |||||
| missense | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| splice region | 2 | 2 | ||||
| non coding | 1 | |||||
| Total | 0 | 0 | 7 | 0 | 2 |
Variants in EIF3D
This is a list of pathogenic ClinVar variants found in the EIF3D region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 22-36511652-A-G | not specified | Uncertain significance (Aug 22, 2023) | ||
| 22-36511662-G-A | not specified | Uncertain significance (Feb 14, 2024) | ||
| 22-36516552-C-T | not specified | Uncertain significance (May 26, 2024) | ||
| 22-36516608-C-G | Uncertain significance (Nov 09, 2023) | |||
| 22-36516762-G-C | not specified | Uncertain significance (Nov 21, 2022) | ||
| 22-36518920-G-A | Benign (Mar 02, 2018) | |||
| 22-36519398-C-T | Benign (Mar 02, 2018) | |||
| 22-36519417-A-G | Benign (Aug 20, 2018) | |||
| 22-36519451-C-T | not specified | Uncertain significance (Mar 19, 2024) | ||
| 22-36519533-A-G | not specified | Uncertain significance (May 28, 2024) | ||
| 22-36523228-T-C | not specified | Uncertain significance (Apr 07, 2022) | ||
| 22-36524637-G-C | not specified | Uncertain significance (Mar 19, 2024) | ||
| 22-36524640-T-G | not specified | Uncertain significance (Feb 06, 2024) | ||
| 22-36525714-G-A | Benign (Aug 20, 2018) | |||
| 22-36526045-C-T | not specified | Uncertain significance (Aug 08, 2023) | ||
| 22-36526074-C-T | EBV-positive nodal T- and NK-cell lymphoma | Likely benign (-) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| EIF3D | protein_coding | protein_coding | ENST00000216190 | 14 | 18587 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000169 | 125741 | 0 | 6 | 125747 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.49 | 158 | 339 | 0.466 | 0.0000212 | 3659 |
| Missense in Polyphen | 36 | 121.87 | 0.29541 | 1316 | ||
| Synonymous | -0.215 | 123 | 120 | 1.02 | 0.00000731 | 969 |
| Loss of Function | 5.05 | 2 | 33.6 | 0.0595 | 0.00000173 | 367 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000214 | 0.000213 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000880 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: mRNA cap-binding component of the eukaryotic translation initiation factor 3 (eIF-3) complex, a complex required for several steps in the initiation of protein synthesis of a specialized repertoire of mRNAs (PubMed:27462815). The eIF-3 complex associates with the 40S ribosome and facilitates the recruitment of eIF-1, eIF-1A, eIF-2:GTP:methionyl-tRNAi and eIF-5 to form the 43S pre-initiation complex (43S PIC). The eIF-3 complex stimulates mRNA recruitment to the 43S PIC and scanning of the mRNA for AUG recognition. The eIF-3 complex is also required for disassembly and recycling of post-termination ribosomal complexes and subsequently prevents premature joining of the 40S and 60S ribosomal subunits prior to initiation (PubMed:18599441, PubMed:25849773). The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation, including cell cycling, differentiation and apoptosis, and uses different modes of RNA stem-loop binding to exert either translational activation or repression (PubMed:25849773). In the eIF-3 complex, EIF3D specifically recognizes and binds the 7-methylguanosine cap of a subset of mRNAs (PubMed:27462815). {ECO:0000269|PubMed:18599441, ECO:0000269|PubMed:25849773, ECO:0000269|PubMed:27462815}.;
- Disease
- DISEASE: Note=Defects in EIF3D are associated with some cancers, such as prostate, breast and colon cancers. Disease susceptibility may be associated with variations affecting the gene represented in this entry. Down-regulation inhibits proliferation of cancers (PubMed:25370813, PubMed:25322666, PubMed:25682860, PubMed:26617750, PubMed:26008152, PubMed:26036682, PubMed:27035563). {ECO:0000269|PubMed:25322666, ECO:0000269|PubMed:25370813, ECO:0000269|PubMed:25682860, ECO:0000269|PubMed:26008152, ECO:0000269|PubMed:26036682, ECO:0000269|PubMed:26617750, ECO:0000269|PubMed:27035563}.;
- Pathway
- RNA transport - Homo sapiens (human);Translation Factors;Formation of the ternary complex, and subsequently, the 43S complex;Translation initiation complex formation;Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S;Eukaryotic Translation Initiation;Translation;Metabolism of proteins;Formation of a pool of free 40S subunits;Ribosomal scanning and start codon recognition;L13a-mediated translational silencing of Ceruloplasmin expression;GTP hydrolysis and joining of the 60S ribosomal subunit;Cap-dependent Translation Initiation
(Consensus)
Recessive Scores
- pRec
- 0.130
Intolerance Scores
- loftool
- 0.0806
- rvis_EVS
- -0.56
- rvis_percentile_EVS
- 19.31
Haploinsufficiency Scores
- pHI
- 0.420
- hipred
- Y
- hipred_score
- 0.793
- ghis
- 0.664
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.946
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Eif3d
- Phenotype
Zebrafish Information Network
- Gene name
- eif3d
- Affected structure
- head
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- formation of cytoplasmic translation initiation complex;cap-dependent translational initiation;translational initiation;positive regulation of translation;IRES-dependent viral translational initiation;viral translational termination-reinitiation;positive regulation of mRNA binding
- Cellular component
- cytosol;eukaryotic translation initiation factor 3 complex;membrane;eukaryotic 43S preinitiation complex;eukaryotic 48S preinitiation complex;eukaryotic translation initiation factor 3 complex, eIF3m
- Molecular function
- RNA binding;translation initiation factor activity;protein binding;mRNA cap binding