E4F1
Basic information
Region (hg38): 16:2223580-2235742
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (123 variants)
- not_provided (2 variants)
- Pyruvate_dehydrogenase_complex_deficiency (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the E4F1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004424.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 116 | 124 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 116 | 9 | 0 |
Highest pathogenic variant AF is 0.0000020549605
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| E4F1 | protein_coding | protein_coding | ENST00000301727 | 14 | 12177 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0801 | 0.920 | 125609 | 0 | 13 | 125622 | 0.0000517 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.35 | 424 | 510 | 0.832 | 0.0000346 | 4988 |
| Missense in Polyphen | 161 | 222.46 | 0.72373 | 2140 | ||
| Synonymous | -2.39 | 279 | 233 | 1.20 | 0.0000177 | 1637 |
| Loss of Function | 3.75 | 8 | 30.3 | 0.264 | 0.00000146 | 364 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000875 | 0.0000875 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000123 | 0.0000544 |
| Finnish | 0.0000468 | 0.0000462 |
| European (Non-Finnish) | 0.0000649 | 0.0000616 |
| Middle Eastern | 0.000123 | 0.0000544 |
| South Asian | 0.0000693 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May function as a transcriptional repressor. May also function as a ubiquitin ligase mediating ubiquitination of chromatin-associated TP53. Functions in cell survival and proliferation through control of the cell cycle. Functions in the p53 and pRB tumor suppressor pathways and regulates the cyclin CCNA2 transcription.;
- Pathway
- p53 pathway
(Consensus)
Recessive Scores
- pRec
- 0.123
Intolerance Scores
- loftool
- 0.187
- rvis_EVS
- -0.73
- rvis_percentile_EVS
- 14.24
Haploinsufficiency Scores
- pHI
- 0.785
- hipred
- Y
- hipred_score
- 0.669
- ghis
- 0.554
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.654
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- E4f1
- Phenotype
- mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- e4f1
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- kinked
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;DNA replication;cell population proliferation;regulation of mitotic cell cycle, embryonic;regulation of cell cycle process;viral process;protein ubiquitination;regulation of growth;cell division;mitotic cell cycle arrest;positive regulation of nucleic acid-templated transcription
- Cellular component
- nucleoplasm;cytoplasm;spindle
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;transcription coactivator activity;transcription corepressor activity;protein binding;transferase activity;cAMP response element binding;metal ion binding