E2F3
E2F transcription factor 3, the group of E2F transcription factors
Basic information
Region (hg38): 6:20401879-20493714
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 E2F3 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 | 12 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 1 | 2 |
Variants in E2F3
This is a list of pathogenic ClinVar variants found in the E2F3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-20402250-G-C | not specified | Uncertain significance (Nov 14, 2023) | ||
| 6-20402254-G-T | not specified | Uncertain significance (Dec 21, 2022) | ||
| 6-20402544-C-G | not specified | Uncertain significance (Mar 28, 2024) | ||
| 6-20402579-C-T | Benign (Sep 09, 2018) | |||
| 6-20482912-G-T | not specified | Uncertain significance (Feb 15, 2023) | ||
| 6-20486716-T-G | not specified | Uncertain significance (Dec 03, 2021) | ||
| 6-20486724-T-G | not specified | Uncertain significance (Jul 28, 2021) | ||
| 6-20488137-A-G | not specified | Uncertain significance (May 30, 2024) | ||
| 6-20488161-T-A | not specified | Uncertain significance (May 16, 2024) | ||
| 6-20488246-A-T | not specified | Uncertain significance (May 28, 2023) | ||
| 6-20490197-G-A | Benign (Mar 01, 2022) | |||
| 6-20490233-G-T | E2F3-related disorder | Likely benign (Apr 04, 2023) | ||
| 6-20490242-G-T | not specified | Uncertain significance (Nov 30, 2022) | ||
| 6-20490294-C-T | not specified | Uncertain significance (May 07, 2024) | ||
| 6-20490302-A-G | not specified | Uncertain significance (Mar 20, 2024) | ||
| 6-20490354-A-G | not specified | Uncertain significance (Apr 09, 2024) | ||
| 6-20490386-G-T | not specified | Uncertain significance (May 23, 2023) | ||
| 6-20490422-T-G | not specified | Uncertain significance (Aug 17, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| E2F3 | protein_coding | protein_coding | ENST00000346618 | 7 | 91544 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.946 | 0.0542 | 125726 | 0 | 6 | 125732 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.59 | 180 | 251 | 0.717 | 0.0000123 | 2963 |
| Missense in Polyphen | 44 | 82.7 | 0.53204 | 975 | ||
| Synonymous | 0.842 | 102 | 113 | 0.899 | 0.00000640 | 982 |
| Loss of Function | 3.50 | 2 | 18.0 | 0.111 | 9.96e-7 | 226 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.000105 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000475 | 0.0000462 |
| European (Non-Finnish) | 0.0000288 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000332 | 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. E2F3 binds specifically to RB1 in a cell-cycle dependent manner. Inhibits adipogenesis, probably through the repression of CEBPA binding to its target gene promoters (By similarity). {ECO:0000250|UniProtKB:O35261}.;
- Pathway
- Non-small cell lung cancer - Homo sapiens (human);Chronic myeloid leukemia - Homo sapiens (human);Gastric cancer - Homo sapiens (human);Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Melanoma - Homo sapiens (human);Cushing,s syndrome - Homo sapiens (human);Bladder cancer - Homo sapiens (human);Cell cycle - Homo sapiens (human);Small cell lung cancer - Homo sapiens (human);Breast cancer - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Glioma - Homo sapiens (human);Prostate cancer - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Hepatitis B - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Pancreatic cancer - Homo sapiens (human);Cell Cycle;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Metastatic brain tumor;B Cell Receptor Signaling Pathway;Retinoblastoma (RB) in Cancer;G1 to S cell cycle control;Signal Transduction;Oncogene Induced Senescence;Oxidative Stress Induced Senescence;Cellular Senescence;Cellular responses to stress;Cyclin D associated events in G1;G1 Phase;Pre-NOTCH Transcription and Translation;Pre-NOTCH Expression and Processing;Mitotic G1-G1/S phases;Signaling by NOTCH;G2 Phase;Cellular responses to external stimuli;Mitotic G2-G2/M phases;Direct p53 effectors;Cell Cycle;Cell Cycle, Mitotic;Validated targets of C-MYC transcriptional activation;Regulation of retinoblastoma protein;E2F transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.0964
Intolerance Scores
- loftool
- 0.289
- rvis_EVS
- 0.35
- rvis_percentile_EVS
- 74.18
Haploinsufficiency Scores
- pHI
- 0.868
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.409
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.993
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- E2f3
- Phenotype
- vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; immune system phenotype; respiratory system phenotype; growth/size/body region phenotype; 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); 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); normal 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); reproductive system phenotype; homeostasis/metabolism phenotype; cellular phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;cell cycle;positive regulation of cell population proliferation;positive regulation of transcription by RNA polymerase II;regulation of cell cycle;negative regulation of fat cell proliferation;positive regulation of vascular associated smooth muscle cell apoptotic process
- Cellular component
- nucleus;nucleoplasm;RNA polymerase II transcription factor complex
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;proximal promoter sequence-specific DNA binding;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding;transcription factor binding;sequence-specific DNA binding;protein dimerization activity