CCNE1
cyclin E1, the group of Cyclins
Basic information
Region (hg38): 19:29811991-29824312
Previous symbols: [ "CCNE" ]
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 CCNE1 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 | 14 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 14 | 3 | 0 |
Variants in CCNE1
This is a list of pathogenic ClinVar variants found in the CCNE1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-29812569-G-T | not specified | Uncertain significance (Jun 10, 2024) | ||
| 19-29812577-C-T | not specified | Uncertain significance (Mar 19, 2024) | ||
| 19-29812774-G-C | not specified | Uncertain significance (Dec 27, 2022) | ||
| 19-29812969-T-C | not specified | Uncertain significance (Sep 01, 2021) | ||
| 19-29812982-C-A | not specified | Uncertain significance (Sep 17, 2021) | ||
| 19-29817188-C-A | not specified | Uncertain significance (Dec 27, 2022) | ||
| 19-29817201-A-G | not specified | Uncertain significance (Dec 20, 2023) | ||
| 19-29817203-G-C | not specified | Uncertain significance (Aug 12, 2021) | ||
| 19-29817275-G-A | not specified | Uncertain significance (Sep 16, 2021) | ||
| 19-29817411-C-G | not specified | Uncertain significance (Sep 23, 2023) | ||
| 19-29817439-G-C | Neoplasm | - (-) | ||
| 19-29820772-C-T | not specified | Uncertain significance (Oct 03, 2023) | ||
| 19-29821812-A-G | not specified | Uncertain significance (Jul 12, 2023) | ||
| 19-29822077-C-T | not specified | Likely benign (Aug 17, 2022) | ||
| 19-29822093-C-T | not specified | Uncertain significance (Aug 16, 2022) | ||
| 19-29822291-A-G | not specified | Likely benign (Sep 13, 2023) | ||
| 19-29822465-A-G | not specified | Uncertain significance (May 08, 2024) | ||
| 19-29822541-A-G | not specified | Uncertain significance (Jan 27, 2022) | ||
| 19-29822571-A-G | not specified | Uncertain significance (Jan 05, 2022) | ||
| 19-29823742-G-A | not specified | Likely benign (May 05, 2023) | ||
| 19-29823760-G-A | not specified | Uncertain significance (Sep 13, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CCNE1 | protein_coding | protein_coding | ENST00000262643 | 11 | 12411 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.972 | 0.0281 | 125741 | 0 | 7 | 125748 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.53 | 168 | 234 | 0.719 | 0.0000123 | 2704 |
| Missense in Polyphen | 52 | 93.577 | 0.55569 | 1136 | ||
| Synonymous | -0.314 | 92 | 88.3 | 1.04 | 0.00000529 | 729 |
| Loss of Function | 4.00 | 3 | 24.3 | 0.124 | 0.00000120 | 284 |
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 | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000440 | 0.0000439 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Essential for the control of the cell cycle at the G1/S (start) transition. {ECO:0000269|PubMed:7739542}.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Gastric cancer - Homo sapiens (human);Cushing,s syndrome - Homo sapiens (human);Cell cycle - Homo sapiens (human);Oocyte meiosis - Homo sapiens (human);p53 signaling pathway - Homo sapiens (human);Small cell lung cancer - Homo sapiens (human);Prostate cancer - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Hepatitis B - Homo sapiens (human);Measles - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Cell Cycle;Androgen receptor signaling pathway;miRNA Regulation of DNA Damage Response;miRNAs involved in DNA damage response;Mitotic G1-G1-S phases;Human Thyroid Stimulating Hormone (TSH) signaling pathway;Signaling Pathways in Glioblastoma;Parkin-Ubiquitin Proteasomal System pathway;Parkinsons Disease Pathway;Retinoblastoma (RB) in Cancer;ATM Signaling Pathway;Vitamin D Receptor Pathway;Photodynamic therapy-induced AP-1 survival signaling.;regulation of p27 phosphorylation during cell cycle progression;PI3K-Akt Signaling Pathway;G1 to S cell cycle control;ID signaling pathway;DNA Damage Response;Signaling by PTK6;RAGE;Signal Transduction;Gene expression (Transcription);cyclin e destruction pathway;influence of ras and rho proteins on g1 to s transition;il-2 receptor beta chain in t cell activation;cell cycle: g1/s check point;cyclins and cell cycle regulation;e2f1 destruction pathway;cdk regulation of dna replication;Generic Transcription Pathway;DNA Damage/Telomere Stress Induced Senescence;Cellular Senescence;Cellular responses to stress;Metabolism of proteins;RNA Polymerase II Transcription;p53-Dependent G1 DNA Damage Response;p53-Dependent G1/S DNA damage checkpoint;G1/S DNA Damage Checkpoints;Chaperonin-mediated protein folding;Cell Cycle Checkpoints;G0 and Early G1;Association of TriC/CCT with target proteins during biosynthesis;SCF(Skp2)-mediated degradation of p27/p21;Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes;Cyclin E associated events during G1/S transition ;Activation of E2F1 target genes at G1/S;G1/S-Specific Transcription;PTK6 Regulates Cell Cycle;Mitotic G1-G1/S phases;Cyclin A:Cdk2-associated events at S phase entry;DNA Replication;Switching of origins to a post-replicative state;AndrogenReceptor;Synthesis of DNA;S Phase;Cellular responses to external stimuli;TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest;p53 signaling pathway;TGF_beta_Receptor;TP53 Regulates Transcription of Cell Cycle Genes;IL2;Protein folding;Signaling by Non-Receptor Tyrosine Kinases;G1/S Transition;Transcriptional Regulation by TP53;CDK-mediated phosphorylation and removal of Cdc6;Cell Cycle;Cell Cycle, Mitotic;mTOR signaling pathway;PLK3 signaling events;BARD1 signaling events;FOXM1 transcription factor network;Regulation of retinoblastoma protein;E2F transcription factor network;Signaling events mediated by PRL
(Consensus)
Recessive Scores
- pRec
- 0.287
Intolerance Scores
- loftool
- 0.441
- rvis_EVS
- -0.36
- rvis_percentile_EVS
- 28.93
Haploinsufficiency Scores
- pHI
- 1.00
- hipred
- Y
- hipred_score
- 0.685
- ghis
- 0.650
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.505
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ccne1
- Phenotype
- embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; 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); 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); neoplasm; 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); digestive/alimentary phenotype; immune system phenotype; skeleton 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; endocrine/exocrine gland phenotype; cellular phenotype;
Gene ontology
- Biological process
- regulation of cyclin-dependent protein serine/threonine kinase activity;G1/S transition of mitotic cell cycle;regulation of transcription involved in G1/S transition of mitotic cell cycle;negative regulation of transcription by RNA polymerase II;mitotic cell cycle;telomere maintenance;DNA replication initiation;protein phosphorylation;regulation of mitotic nuclear division;synapsis;positive regulation of cell population proliferation;Wnt signaling pathway;androgen receptor signaling pathway;positive regulation of cell cycle;positive regulation of transcription, DNA-templated;cell division;positive regulation of G1/S transition of mitotic cell cycle;regulation of cellular protein localization
- Cellular component
- cyclin-dependent protein kinase holoenzyme complex;nucleus;nucleoplasm;cytoplasm;centrosome;cytosol;cyclin E1-CDK2 complex
- Molecular function
- transcription coactivator activity;protein kinase activity;cyclin-dependent protein serine/threonine kinase activity;protein binding;cyclin-dependent protein serine/threonine kinase regulator activity;protein kinase binding;androgen receptor binding