EIF5A2
Basic information
Region (hg38): 3:170888418-170908644
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 EIF5A2 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 | 0 | |||||
| missense | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 0 | 0 |
Variants in EIF5A2
This is a list of pathogenic ClinVar variants found in the EIF5A2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-170893377-T-C | not specified | Uncertain significance (Aug 17, 2021) | ||
| 3-170893408-C-G | not specified | Uncertain significance (Jun 23, 2021) | ||
| 3-170894297-C-G | not specified | Uncertain significance (May 23, 2024) | ||
| 3-170894311-T-C | not specified | Uncertain significance (Dec 11, 2023) | ||
| 3-170907089-T-C | not specified | Uncertain significance (Sep 14, 2022) | ||
| 3-170907700-C-T | not specified | Uncertain significance (Mar 22, 2023) | ||
| 3-170907797-C-T | not specified | Uncertain significance (Oct 12, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| EIF5A2 | protein_coding | protein_coding | ENST00000295822 | 4 | 20279 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000211 | 0.513 | 125737 | 0 | 11 | 125748 | 0.0000437 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.24 | 53 | 85.1 | 0.623 | 0.00000419 | 1000 |
| Missense in Polyphen | 9 | 17.365 | 0.51827 | 234 | ||
| Synonymous | 0.299 | 27 | 29.1 | 0.929 | 0.00000156 | 285 |
| Loss of Function | 0.404 | 6 | 7.17 | 0.837 | 3.73e-7 | 90 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000290 | 0.0000290 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000545 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000706 | 0.0000703 |
| Middle Eastern | 0.0000545 | 0.0000544 |
| South Asian | 0.0000332 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: mRNA-binding protein involved in translation elongation. Has an important function at the level of mRNA turnover, probably acting downstream of decapping. Involved in actin dynamics and cell cycle progression, mRNA decay and probably in a pathway involved in stress response and maintenance of cell wall integrity. Functions as a regulator of apoptosis. Mediates effects of polyamines on neuronal process extension and survival. May play an important role in brain development and function, and in skeletal muscle stem cell differentiation (By similarity). {ECO:0000250, ECO:0000269|PubMed:14622290}.;
- Pathway
- EMT transition in Colorectal Cancer;Post-translational protein modification;Metabolism of proteins;Gamma carboxylation, hypusine formation and arylsulfatase activation;Hypusine synthesis from eIF5A-lysine
(Consensus)
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- loftool
- 0.540
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 59.43
Haploinsufficiency Scores
- pHI
- 0.492
- hipred
- N
- hipred_score
- 0.459
- ghis
- 0.601
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.781
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Eif5a2
- Phenotype
- normal phenotype;
Gene ontology
- Biological process
- translational frameshifting;spermatogenesis;positive regulation of cell population proliferation;polyamine homeostasis;protein transport;positive regulation of translational elongation;positive regulation of translational termination;mRNA transport
- Cellular component
- nuclear pore;endoplasmic reticulum membrane;cytosol;intracellular membrane-bounded organelle
- Molecular function
- translation elongation factor activity;protein binding;ribosome binding