CCNE2
cyclin E2, the group of Cyclins
Basic information
Region (hg38): 8:94879770-94896678
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 CCNE2 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 | 17 | 18 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 17 | 1 | 0 |
Variants in CCNE2
This is a list of pathogenic ClinVar variants found in the CCNE2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-94880161-AAGAAGTGTT-A | Neurodevelopmental disorder with cerebellar hypoplasia and spasticity | Pathogenic (Sep 11, 2019) | ||
| 8-94881643-C-T | not specified | Uncertain significance (Dec 19, 2022) | ||
| 8-94881646-G-A | not specified | Uncertain significance (Jan 18, 2025) | ||
| 8-94882169-T-C | not specified | Uncertain significance (Mar 02, 2023) | ||
| 8-94882170-G-A | not specified | Uncertain significance (Apr 15, 2024) | ||
| 8-94882199-G-A | not specified | Likely benign (Feb 12, 2025) | ||
| 8-94882266-C-G | not specified | Uncertain significance (Nov 15, 2024) | ||
| 8-94882795-A-C | not specified | Uncertain significance (Jan 02, 2025) | ||
| 8-94882804-A-G | not specified | Uncertain significance (Nov 25, 2024) | ||
| 8-94882817-G-A | not specified | Uncertain significance (Sep 26, 2024) | ||
| 8-94882892-G-A | not specified | Uncertain significance (Mar 03, 2025) | ||
| 8-94885087-T-C | not specified | Uncertain significance (Oct 17, 2024) | ||
| 8-94885110-A-C | not specified | Uncertain significance (Jan 02, 2025) | ||
| 8-94885125-T-C | not specified | Uncertain significance (May 08, 2024) | ||
| 8-94885171-T-C | not specified | Likely benign (May 12, 2024) | ||
| 8-94885464-T-G | not specified | Uncertain significance (Jun 06, 2023) | ||
| 8-94885498-C-T | not specified | Uncertain significance (Jan 23, 2023) | ||
| 8-94885529-A-C | not specified | Uncertain significance (Sep 02, 2024) | ||
| 8-94885548-G-C | not specified | Uncertain significance (Jun 11, 2024) | ||
| 8-94888052-G-A | not specified | Uncertain significance (Oct 12, 2021) | ||
| 8-94888057-G-A | not specified | Uncertain significance (Apr 01, 2024) | ||
| 8-94892829-C-A | not specified | Uncertain significance (Jun 12, 2023) | ||
| 8-94892852-G-T | not specified | Uncertain significance (Mar 01, 2023) | ||
| 8-94892908-T-G | not specified | Uncertain significance (Feb 01, 2025) | ||
| 8-94894040-T-G | not specified | Uncertain significance (Jul 20, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CCNE2 | protein_coding | protein_coding | ENST00000520509 | 11 | 16909 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.870 | 0.130 | 125737 | 0 | 9 | 125746 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.50 | 140 | 200 | 0.701 | 0.00000875 | 2668 |
| Missense in Polyphen | 39 | 72.646 | 0.53685 | 1002 | ||
| Synonymous | 0.876 | 57 | 66.1 | 0.863 | 0.00000306 | 703 |
| Loss of Function | 3.81 | 4 | 24.3 | 0.165 | 0.00000103 | 310 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000125 | 0.000125 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000565 | 0.0000544 |
| Finnish | 0.000141 | 0.000139 |
| European (Non-Finnish) | 0.0000178 | 0.0000176 |
| Middle Eastern | 0.0000565 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Essential for the control of the cell cycle at the late G1 and early S phase.;
- 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;miRNA Regulation of DNA Damage Response;Parkinsons Disease Pathway;Retinoblastoma (RB) in Cancer;PI3K-Akt Signaling Pathway;G1 to S cell cycle control;DNA Damage Response;Gene expression (Transcription);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;p73 transcription factor network;Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes;Cyclin E associated events during G1/S transition ;Mitotic G1-G1/S phases;Cyclin A:Cdk2-associated events at S phase entry;DNA Replication;Switching of origins to a post-replicative state;Synthesis of DNA;S Phase;Cellular responses to external stimuli;TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest;TP53 Regulates Transcription of Cell Cycle Genes;Protein folding;G1/S Transition;Transcriptional Regulation by TP53;CDK-mediated phosphorylation and removal of Cdc6;Cell Cycle;Cell Cycle, Mitotic;E2F transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.168
Intolerance Scores
- loftool
- 0.676
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 53.51
Haploinsufficiency Scores
- pHI
- 0.996
- hipred
- Y
- hipred_score
- 0.749
- ghis
- 0.586
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.872
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ccne2
- 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; 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); growth/size/body region phenotype; 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); cellular phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- regulation of cyclin-dependent protein serine/threonine kinase activity;G1/S transition of mitotic cell cycle;mitotic cell cycle;telomere maintenance;DNA replication initiation;protein phosphorylation;regulation of mitotic nuclear division;synapsis;positive regulation of cell population proliferation;positive regulation of cell cycle;cell division;regulation of cellular protein localization
- Cellular component
- cyclin-dependent protein kinase holoenzyme complex;nucleus;nucleoplasm;cytoplasm;centrosome;cytosol;cyclin E2-CDK2 complex
- Molecular function
- protein kinase activity;cyclin-dependent protein serine/threonine kinase activity;protein binding;cyclin-dependent protein serine/threonine kinase regulator activity;protein kinase binding