CDC25C
protein-codingcell division cycle 25C, the group of Protein phosphatase 1 regulatory subunits|Class III Cys-based CDC25 phosphatases
Gene summary
This gene encodes a conserved protein that plays a key role in the regulation of cell division. The encoded protein directs dephosphorylation of cyclin B-bound CDC2 and triggers entry into mitosis. It also suppresses p53-induced growth arrest. Multiple alternatively spliced transcript variants of this gene have been described. [provided by RefSeq, Dec 2015]
- CDC25
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~53.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CDC25C variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001790.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | 2 | |||
| missense | 70 | 2 | 72 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 74 | 3 | 0 | 77 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001781.2 | 13 | MANE Select | |
| Ensembl | ENSP00000321656.6 | 13 | MANE Select | |
| RefSeq | NP_001274511.1 | 13 | Standard | |
| RefSeq | NP_001274512.1 | 14 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Cell cycle - Homo sapiens (human)
- Oocyte meiosis - Homo sapiens (human)
- MicroRNAs in cancer - Homo sapiens (human)
- Progesterone-mediated oocyte maturation - Homo sapiens (human)
- Cell Cycle
Biological Process
- regulation of cyclin-dependent protein serine/threonine kinase activity
- G2/M transition of mitotic cell cycle
- DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
- regulation of mitotic nuclear division
- spermatogenesis
Molecular Function
- phosphoprotein phosphatase activity
- protein tyrosine phosphatase activity
- protein binding
- protein kinase binding
- WW domain binding
Cellular Component
- nucleus
- nucleoplasm
- cytoplasm
- cytosol
- nuclear speck
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000323760
- Coding exons
- 13
- Length
- 53091
- Individuals with no LoFs
- 125685
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 62
- Defined
- 125747
- p
- 0.000247
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.753 | 224 | 258 | 0.868 | 0.0000132 | 3112 |
| Missense (PolyPhen) | 68 | 76.685 | 0.88675 | 933 | ||
| Synonymous | 0.859 | 87 | 97.8 | 0.890 | 0.00000507 | 874 |
| Loss of Function | 0.619 | 21 | 24.3 | 0.864 | 0.00000110 | 336 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0015 | 0.0015 | notable |
| Latino/Admixed American | 0.000092 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000071 | 0.000070 | rare |
| South Asian | 0.00080 | 0.00078 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Functions as a dosage-dependent inducer in mitotic control. Tyrosine protein phosphatase required for progression of the cell cycle. When phosphorylated, highly effective in activating G2 cells into prophase. Directly dephosphorylates CDK1 and activates its kinase activity. {ECO:0000269|PubMed:8119945}.;
Recessive Scores
- pRec
- 0.420
Intolerance Scores
- LoFtool
- 0.971
- RVIS EVS
- -0.02
- RVIS percentile EVS
- 52.09
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.000611
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |