CDC25B
cell division cycle 25B, the group of Class III Cys-based CDC25 phosphatases
Basic information
Region (hg38): 20:3786772-3806121
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (82 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDC25B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021873.4. 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 | 2 | |||||
| missense | 75 | 81 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 75 | 8 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CDC25B | protein_coding | protein_coding | ENST00000245960 | 16 | 19185 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.364 | 0.636 | 125729 | 0 | 17 | 125746 | 0.0000676 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.47 | 291 | 371 | 0.785 | 0.0000243 | 3768 |
| Missense in Polyphen | 97 | 150.47 | 0.64465 | 1450 | ||
| Synonymous | -0.832 | 156 | 143 | 1.09 | 0.00000911 | 1140 |
| Loss of Function | 3.99 | 7 | 30.9 | 0.226 | 0.00000172 | 339 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000188 | 0.000188 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000974 | 0.0000967 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Tyrosine protein phosphatase which functions as a dosage-dependent inducer of mitotic progression. Required for G2/M phases of the cell cycle progression and abscission during cytokinesis in a ECT2-dependent manner. Directly dephosphorylates CDK1 and stimulates its kinase activity. The three isoforms seem to have a different level of activity. {ECO:0000269|PubMed:17332740}.;
- Pathway
- Cell cycle - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Progesterone-mediated oocyte maturation - Homo sapiens (human);Cell Cycle;Integrated Cancer Pathway;Androgen Receptor Network in Prostate Cancer;Retinoblastoma (RB) in Cancer;MAPK Signaling Pathway;Senescence and Autophagy in Cancer;Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer,s disease models;Neurodegenerative Diseases;Disease;Cyclin A:Cdk2-associated events at S phase entry;AndrogenReceptor;Aurora A signaling;S Phase;Cyclin A/B1/B2 associated events during G2/M transition;G2/M Transition;Mitotic G2-G2/M phases;Cell Cycle;Cell Cycle, Mitotic;PLK1 signaling events;FOXM1 transcription factor network;p38 signaling mediated by MAPKAP kinases
(Consensus)
Recessive Scores
- pRec
- 0.183
Intolerance Scores
- loftool
- 0.577
- rvis_EVS
- -1.13
- rvis_percentile_EVS
- 6.48
Haploinsufficiency Scores
- pHI
- 0.608
- hipred
- Y
- hipred_score
- 0.731
- ghis
- 0.564
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.600
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cdc25b
- Phenotype
- digestive/alimentary phenotype; growth/size/body region phenotype; 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); cellular phenotype; endocrine/exocrine gland phenotype;
Zebrafish Information Network
- Gene name
- cdc25b
- Affected structure
- pigment cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- G2/M transition of mitotic cell cycle;mitotic cell cycle;oocyte maturation;protein phosphorylation;female meiosis I;positive regulation of cell population proliferation;positive regulation of G2/M transition of mitotic cell cycle;positive regulation of cytokinesis;peptidyl-tyrosine dephosphorylation;positive regulation of protein kinase activity;positive regulation of mitotic cell cycle;cell division;positive regulation of G2/MI transition of meiotic cell cycle
- Cellular component
- spindle pole;nucleus;nucleoplasm;cytoplasm;centrosome;cytosol
- Molecular function
- phosphoprotein phosphatase activity;protein tyrosine phosphatase activity;protein binding;protein kinase binding