E2F1
E2F transcription factor 1, the group of E2F transcription factors
Basic information
Region (hg38): 20:33675477-33686385
Previous symbols: [ "RBBP3" ]
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 E2F1 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 | 10 | |||||
| missense | 10 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 2 | |||||
| Total | 0 | 0 | 10 | 8 | 9 |
Variants in E2F1
This is a list of pathogenic ClinVar variants found in the E2F1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 20-33676727-C-A | E2F1-related disorder | Benign (Mar 06, 2019) | ||
| 20-33676801-G-A | E2F1-related disorder | Likely benign (Sep 10, 2019) | ||
| 20-33676807-G-A | E2F1-related disorder | Likely benign (Jul 01, 2019) | ||
| 20-33676859-G-C | Inborn genetic diseases | Uncertain significance (Jan 31, 2023) | ||
| 20-33676869-C-T | E2F1-related disorder | Benign (Apr 09, 2019) | ||
| 20-33676870-G-A | E2F1-related disorder | Likely benign (Jun 14, 2019) | ||
| 20-33676901-G-A | not specified | Uncertain significance (Aug 17, 2021) | ||
| 20-33676905-C-T | not specified | Uncertain significance (Apr 19, 2023) | ||
| 20-33676909-C-T | Benign (Dec 31, 2019) | |||
| 20-33677143-G-A | not specified | Uncertain significance (Aug 13, 2021) | ||
| 20-33677154-G-A | E2F1-related disorder | Likely benign (Mar 19, 2019) | ||
| 20-33677213-C-T | not specified | Uncertain significance (Jun 17, 2024) | ||
| 20-33677440-C-T | E2F1-related disorder | Benign (Sep 18, 2018) | ||
| 20-33677441-G-A | Likely benign (Sep 05, 2018) | |||
| 20-33677525-C-T | E2F1-related disorder | Benign (Jun 18, 2019) | ||
| 20-33678328-C-T | E2F1-related disorder | Benign (Sep 17, 2019) | ||
| 20-33679830-C-T | Malignant tumor of prostate | Uncertain significance (-) | ||
| 20-33679965-G-T | not specified | Uncertain significance (May 20, 2024) | ||
| 20-33680374-C-T | E2F1-related disorder | Likely benign (Dec 31, 2019) | ||
| 20-33685994-G-A | Likely benign (Dec 31, 2019) | |||
| 20-33686031-C-G | Benign (Sep 18, 2018) | |||
| 20-33686033-C-A | not specified | Uncertain significance (May 08, 2023) | ||
| 20-33686034-A-C | not specified | Uncertain significance (Jan 03, 2024) | ||
| 20-33686039-G-A | not specified | Uncertain significance (Dec 02, 2022) | ||
| 20-33686066-C-G | not specified | Uncertain significance (Mar 21, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| E2F1 | protein_coding | protein_coding | ENST00000343380 | 7 | 10722 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.988 | 0.0123 | 125473 | 0 | 1 | 125474 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.07 | 129 | 214 | 0.602 | 0.0000138 | 2765 |
| Missense in Polyphen | 30 | 78.781 | 0.3808 | 965 | ||
| Synonymous | 0.880 | 87 | 98.1 | 0.887 | 0.00000685 | 958 |
| Loss of Function | 3.38 | 0 | 13.3 | 0.00 | 5.67e-7 | 168 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| 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. E2F1 binds preferentially RB1 in a cell-cycle dependent manner. It can mediate both cell proliferation and TP53/p53-dependent apoptosis. Blocks adipocyte differentiation by binding to specific promoters repressing CEBPA binding to its target gene promoters (PubMed:20176812). Positively regulates transcription of RRP1B (PubMed:20040599). {ECO:0000250|UniProtKB:Q61501, ECO:0000269|PubMed:10675335, ECO:0000269|PubMed:12717439, ECO:0000269|PubMed:17704056, ECO:0000269|PubMed:20040599, ECO:0000269|PubMed:20176812, ECO:0000269|PubMed:8170954}.;
- 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);Mitophagy - animal - 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);Human papillomavirus infection - Homo sapiens (human);Cell Cycle;miRNA Regulation of DNA Damage Response;miRNAs involved in DNA damage response;Integrated Breast Cancer Pathway;miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Mitotic G1-G1-S phases;Human Thyroid Stimulating Hormone (TSH) signaling pathway;Signaling Pathways in Glioblastoma;Adipogenesis;Spinal Cord Injury;Retinoblastoma (RB) in Cancer;Aryl Hydrocarbon Receptor;Mammary gland development pathway - Involution (Stage 4 of 4);Bladder Cancer;MECP2 and Associated Rett Syndrome;regulation of p27 phosphorylation during cell cycle progression;TP53 Regulates Transcription of Cell Cycle Genes;H19 action Rb-E2F1 signaling and CDK-β-catenin activity;Prader-Willi and Angelman Syndrome;EGF-EGFR Signaling Pathway;G1 to S cell cycle control;Senescence and Autophagy in Cancer;DNA Damage Response;Signal Transduction;Gene expression (Transcription);Inhibition of replication initiation of damaged DNA by RB1/E2F1;cyclin e destruction pathway;influence of ras and rho proteins on g1 to s transition;tumor suppressor arf inhibits ribosomal biogenesis;il-2 receptor beta chain in t cell activation;cell cycle: g1/s check point;cyclins and cell cycle regulation;e2f1 destruction pathway;mets affect on macrophage differentiation;Transcriptional Regulation by E2F6;Generic Transcription Pathway;Oncogene Induced Senescence;Oxidative Stress Induced Senescence;Cellular Senescence;Cellular responses to stress;RNA Polymerase II Transcription;Activation of NOXA and translocation to mitochondria;Activation of PUMA and translocation to mitochondria;Activation of BH3-only proteins;Intrinsic Pathway for Apoptosis;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;Apoptosis;Programmed Cell Death;Cyclin D associated events in G1;G1 Phase;Activation of E2F1 target genes at G1/S;G1/S-Specific Transcription;Pre-NOTCH Transcription and Translation;Pre-NOTCH Expression and Processing;E2F mediated regulation of DNA replication;Mitotic G1-G1/S phases;Signaling by NOTCH;G2 Phase;Cellular responses to external stimuli;TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest;p53 signaling pathway;TP53 Regulates Transcription of Cell Cycle Genes;rb tumor suppressor/checkpoint signaling in response to dna damage;Mitotic G2-G2/M phases;G1/S Transition;Transcriptional Regulation by TP53;Direct p53 effectors;Cell Cycle;Cell Cycle, Mitotic;Notch-mediated HES/HEY network;Calcineurin-regulated NFAT-dependent transcription in lymphocytes;Regulation of Telomerase;IL2 signaling events mediated by PI3K;p75(NTR)-mediated signaling;Regulation of retinoblastoma protein;E2F transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.791
Intolerance Scores
- loftool
- rvis_EVS
- 0.31
- rvis_percentile_EVS
- 72.38
Haploinsufficiency Scores
- pHI
- 0.993
- hipred
- Y
- hipred_score
- 0.831
- ghis
- 0.519
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
- E2f1
- Phenotype
- digestive/alimentary 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); hearing/vestibular/ear phenotype; vision/eye phenotype; immune system phenotype; skeleton phenotype; embryo phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system 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); reproductive 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; 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); neoplasm; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); muscle phenotype; craniofacial phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- e2f1
- Affected structure
- thymus
- Phenotype tag
- abnormal
- Phenotype quality
- increased amount
Gene ontology
- Biological process
- DNA damage checkpoint;regulation of transcription involved in G1/S transition of mitotic cell cycle;negative regulation of transcription by RNA polymerase II;transcription, DNA-templated;regulation of transcription, DNA-templated;DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;spermatogenesis;intrinsic apoptotic signaling pathway in response to DNA damage;positive regulation of gene expression;forebrain development;positive regulation of apoptotic process;anoikis;negative regulation of DNA binding;negative regulation of fat cell differentiation;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of fibroblast proliferation;mRNA stabilization;regulation of cell cycle;positive regulation of glial cell proliferation;negative regulation of G0 to G1 transition;negative regulation of fat cell proliferation;cellular response to fatty acid;cellular response to hypoxia;cellular response to xenobiotic stimulus;negative regulation of transcription involved in G1/S transition of mitotic cell cycle;intrinsic apoptotic signaling pathway by p53 class mediator;positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway;lens fiber cell apoptotic process;cellular response to nerve growth factor stimulus;regulation of G1/S transition of mitotic cell cycle
- Cellular component
- nuclear chromatin;nucleus;nucleoplasm;mitochondrion;centrosome;protein-containing complex;Rb-E2F complex;RNA polymerase II transcription factor complex
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;proximal promoter sequence-specific DNA binding;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding;transcription factor binding;protein kinase binding;sequence-specific DNA binding;protein dimerization activity