E2F4
E2F transcription factor 4, the group of E2F transcription factors
Basic information
Region (hg38): 16:67192155-67198918
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 E2F4 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 | 29 | 29 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 29 | 0 | 1 |
Variants in E2F4
This is a list of pathogenic ClinVar variants found in the E2F4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 16-67192232-C-G | not specified | Uncertain significance (Jul 11, 2023) | ||
| 16-67192241-G-T | not specified | Uncertain significance (Dec 17, 2023) | ||
| 16-67192271-C-G | not specified | Uncertain significance (Dec 07, 2021) | ||
| 16-67193055-A-G | not specified | Uncertain significance (Aug 01, 2024) | ||
| 16-67193079-G-A | not specified | Uncertain significance (Nov 21, 2022) | ||
| 16-67193164-A-G | not specified | Uncertain significance (Aug 28, 2023) | ||
| 16-67193512-G-A | not specified | Uncertain significance (Aug 04, 2024) | ||
| 16-67194687-G-T | not specified | Uncertain significance (Jul 14, 2021) | ||
| 16-67194689-C-T | not specified | Uncertain significance (Feb 28, 2024) | ||
| 16-67194729-T-C | not specified | Uncertain significance (Jun 07, 2024) | ||
| 16-67194774-G-A | not specified | Uncertain significance (Sep 10, 2024) | ||
| 16-67194798-T-A | not specified | Uncertain significance (Jan 19, 2022) | ||
| 16-67194801-C-A | not specified | Uncertain significance (Jan 19, 2022) | ||
| 16-67194804-C-T | not specified | Uncertain significance (Oct 07, 2024) | ||
| 16-67194806-C-T | not specified | Uncertain significance (Jan 19, 2022) | ||
| 16-67194887-G-C | not specified | Uncertain significance (Jul 27, 2024) | ||
| 16-67194888-C-G | not specified | Uncertain significance (Sep 29, 2023) | ||
| 16-67194893-C-T | not specified | Uncertain significance (Apr 26, 2023) | ||
| 16-67194894-G-A | not specified | Uncertain significance (Apr 25, 2022) | ||
| 16-67195787-G-A | not specified | Uncertain significance (Sep 14, 2022) | ||
| 16-67195875-C-G | not specified | Uncertain significance (Mar 14, 2023) | ||
| 16-67195890-ACAGCAG-A | Benign (Feb 01, 2023) | |||
| 16-67195929-G-A | not specified | Uncertain significance (Dec 05, 2022) | ||
| 16-67195982-C-G | not specified | Uncertain significance (May 13, 2024) | ||
| 16-67195997-C-A | not specified | Uncertain significance (Dec 01, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| E2F4 | protein_coding | protein_coding | ENST00000379378 | 10 | 6750 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.453 | 0.547 | 125741 | 0 | 6 | 125747 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.08 | 172 | 217 | 0.793 | 0.0000114 | 2653 |
| Missense in Polyphen | 25 | 53.164 | 0.47024 | 692 | ||
| Synonymous | -1.59 | 105 | 86.2 | 1.22 | 0.00000481 | 829 |
| Loss of Function | 3.15 | 4 | 18.7 | 0.214 | 8.95e-7 | 221 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.000199 | 0.000198 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000478 | 0.0000462 |
| European (Non-Finnish) | 0.0000177 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription activator that binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC- 3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The DRTF1/E2F complex functions in the control of cell-cycle progression from G1 to S phase. E2F4 binds with high affinity to RBL1 and RBL2. In some instances can also bind RB1. Specifically required for multiciliate cell differentiation: together with MCIDAS and E2F5, binds and activate genes required for centriole biogenesis. {ECO:0000250|UniProtKB:Q6DE14, ECO:0000269|PubMed:7958924, ECO:0000269|PubMed:7958925}.;
- Pathway
- TGF-beta signaling pathway - Homo sapiens (human);Cell cycle - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Cell Cycle;Adipogenesis;TGF-beta Signaling Pathway;G1 to S cell cycle control;Signal Transduction;Gene expression (Transcription);mets affect on macrophage differentiation;Generic Transcription Pathway;RNA Polymerase II Transcription;Transcription of E2F targets under negative control by DREAM complex;Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1;G0 and Early G1;Cyclin D associated events in G1;G1 Phase;SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription;Mitotic G1-G1/S phases;TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest;TGF_beta_Receptor;Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer;TP53 Regulates Transcription of Cell Cycle Genes;Transcriptional Regulation by TP53;Cell Cycle;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;Cell Cycle, Mitotic;Regulation of retinoblastoma protein;E2F transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.298
Intolerance Scores
- loftool
- 0.126
- rvis_EVS
- -0.74
- rvis_percentile_EVS
- 13.94
Haploinsufficiency Scores
- pHI
- 0.875
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.656
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- E2f4
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; embryo phenotype; neoplasm; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system 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); normal phenotype; reproductive system phenotype; digestive/alimentary phenotype; hearing/vestibular/ear phenotype; skeleton phenotype; homeostasis/metabolism phenotype; immune system phenotype; cellular phenotype; taste/olfaction phenotype; endocrine/exocrine gland phenotype; growth/size/body region 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); craniofacial phenotype;
Gene ontology
- Biological process
- regulation of transcription involved in G1/S transition of mitotic cell cycle;negative regulation of transcription by RNA polymerase II;epithelial cell development;cell volume homeostasis;DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;blood circulation;animal organ morphogenesis;regulation of cell population proliferation;motile cilium assembly;positive regulation of transcription by RNA polymerase II;regulation of cell cycle;centriole assembly;multi-ciliated epithelial cell differentiation
- Cellular component
- nuclear chromatin;nucleus;nucleoplasm;RNA polymerase II transcription factor complex
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding;transcription factor binding;protein domain specific binding;sequence-specific DNA binding;protein dimerization activity;promoter-specific chromatin binding