CDC25A
cell division cycle 25A, the group of Class III Cys-based CDC25 phosphatases
Basic information
Region (hg38): 3:48157146-48188417
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (43 variants)
- Autosomal_dominant_polycystic_liver_disease (4 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDC25A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001789.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 39 | 46 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 39 | 5 | 1 |
Highest pathogenic variant AF is 0.000115186
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CDC25A | protein_coding | protein_coding | ENST00000302506 | 15 | 31257 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.840 | 0.160 | 125736 | 0 | 10 | 125746 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.22 | 179 | 284 | 0.630 | 0.0000148 | 3432 |
| Missense in Polyphen | 46 | 116.5 | 0.39485 | 1330 | ||
| Synonymous | -0.287 | 107 | 103 | 1.04 | 0.00000520 | 979 |
| Loss of Function | 4.03 | 5 | 28.0 | 0.178 | 0.00000143 | 353 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.000105 | 0.0000992 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000535 | 0.0000527 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Tyrosine protein phosphatase which functions as a dosage-dependent inducer of mitotic progression. Directly dephosphorylates CDK1 and stimulates its kinase activity. Also dephosphorylates CDK2 in complex with cyclin E, in vitro.;
- Pathway
- Cell cycle - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Progesterone-mediated oocyte maturation - Homo sapiens (human);Cell Cycle;miRNA Regulation of DNA Damage Response;miRNAs involved in DNA damage response;Integrated Cancer Pathway;Integrated Breast Cancer Pathway;Mitotic G1-G1-S phases;Mitotic G2-G2-M phases;Androgen Receptor Network in Prostate Cancer;Retinoblastoma (RB) in Cancer;ATM Signaling Pathway;S Phase;G1 to S cell cycle control;DNA Damage Response;Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer,s disease models;Neurodegenerative Diseases;Disease;cell cycle: g1/s check point;cyclins and cell cycle regulation;Post-translational protein modification;Metabolism of proteins;Ubiquitin Mediated Degradation of Phosphorylated Cdc25A;p53-Independent DNA Damage Response;p53-Independent G1/S DNA damage checkpoint;G1/S DNA Damage Checkpoints;Activation of ATR in response to replication stress;G2/M Checkpoints;Polo-like kinase mediated events;Cell Cycle Checkpoints;Transcription of E2F targets under negative control by DREAM complex;G0 and Early G1;Cyclin E associated events during G1/S transition ;Activation of E2F1 target genes at G1/S;G1/S-Specific Transcription;Mitotic G1-G1/S phases;Cyclin A:Cdk2-associated events at S phase entry;AndrogenReceptor;S Phase;Cyclin A/B1/B2 associated events during G2/M transition;TGF_beta_Receptor;Ub-specific processing proteases;G2/M Transition;Mitotic G2-G2/M phases;Deubiquitination;G1/S Transition;Cell Cycle;Cell Cycle, Mitotic;Validated targets of C-MYC transcriptional activation;ATM pathway;ATR signaling pathway;E2F transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.373
Intolerance Scores
- loftool
- 0.358
- rvis_EVS
- -0.29
- rvis_percentile_EVS
- 33.2
Haploinsufficiency Scores
- pHI
- 0.999
- hipred
- Y
- hipred_score
- 0.798
- ghis
- 0.628
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- N
- 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
- Cdc25a
- Phenotype
- cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; skeleton phenotype; digestive/alimentary 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; hematopoietic system phenotype; neoplasm; embryo phenotype;
Gene ontology
- Biological process
- regulation of cyclin-dependent protein serine/threonine kinase activity;G1/S transition of mitotic cell cycle;G2/M transition of mitotic cell cycle;cell population proliferation;response to radiation;positive regulation of G2/M transition of mitotic cell cycle;protein deubiquitination;cellular response to UV;peptidyl-tyrosine dephosphorylation;positive regulation of mitotic cell cycle;cell division;regulation of cell cycle;positive regulation of G2/MI transition of meiotic cell cycle
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol
- Molecular function
- phosphoprotein phosphatase activity;protein tyrosine phosphatase activity;protein binding;protein kinase binding;chaperone binding