CDC25C

cell division cycle 25C, the group of Protein phosphatase 1 regulatory subunits|Class III Cys-based CDC25 phosphatases

Basic information

Region (hg38): 5:138285269-138338355

Previous symbols: [ "CDC25" ]

Links

ENSG00000158402 ∙ NCBI:995 ∙ OMIM:157680 ∙ HGNC:1727 ∙ Uniprot:P30307 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDC25C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDC25C 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				1		1
missense			27	2		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	3	0

Variants in CDC25C

This is a list of pathogenic ClinVar variants found in the CDC25C region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-138285717-A-G		not specified	Uncertain significance (Oct 04, 2022)
5-138285733-G-A		not specified	Uncertain significance (Nov 08, 2022)
5-138285763-T-C		not specified	Uncertain significance (Jan 11, 2023)
5-138285792-T-C		not specified	Uncertain significance (Oct 26, 2022)
5-138285811-T-C		not specified	Uncertain significance (Aug 11, 2023)
5-138286033-G-T		not specified	Uncertain significance (Jun 03, 2024)
5-138286053-C-T		not specified	Uncertain significance (Jul 09, 2021)
5-138286098-T-C		not specified	Uncertain significance (Feb 06, 2024)
5-138286111-C-T		not specified	Uncertain significance (Sep 16, 2021)
5-138286119-C-T		not specified	Uncertain significance (Feb 17, 2022)
5-138286512-T-C		not specified	Uncertain significance (Jun 22, 2023)
5-138286570-C-T		not specified	Uncertain significance (Nov 03, 2022)
5-138287221-A-C		not specified	Uncertain significance (Jun 21, 2022)
5-138289520-T-G		not specified	Uncertain significance (Jun 04, 2024)
5-138289545-C-T		not specified	Uncertain significance (Aug 12, 2021)
5-138289546-G-A			Likely benign (Dec 31, 2019)
5-138289556-G-A		not specified	Likely benign (May 17, 2023)
5-138291998-T-C		not specified	Uncertain significance (Nov 21, 2023)
5-138292034-T-C		not specified	Uncertain significance (May 27, 2022)
5-138292088-G-A		not specified	Uncertain significance (Feb 28, 2024)
5-138292091-G-A		not specified	Uncertain significance (Aug 29, 2022)
5-138292109-C-T		not specified	Uncertain significance (Nov 08, 2021)
5-138319232-T-G		not specified	Uncertain significance (Aug 12, 2021)
5-138319277-T-G		not specified	Uncertain significance (Jan 02, 2024)
5-138325867-C-T		not specified	Likely benign (Jul 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDC25C	protein_coding	protein_coding	ENST00000323760	13	53091

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.10e-13	0.0910	125685	0	62	125747	0.000247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.753	224	258	0.868	0.0000132	3112
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00158	0.00157
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000707	0.0000703
Middle Eastern	0.000164	0.000163
South Asian	0.000797	0.000784
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: 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;miRNA Regulation of DNA Damage Response;ATM Signaling Pathway;TP53 Regulates Transcription of Cell Cycle Genes;DNA Damage Response;Monoamine Transport;Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer,s disease models;Neurodegenerative Diseases;Disease;Signal Transduction;Gene expression (Transcription);how progesterone initiates the oocyte maturation;Generic Transcription Pathway;Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex;RNA Polymerase II Transcription;G2/M DNA damage checkpoint;Activation of ATR in response to replication stress;G2/M Checkpoints;Polo-like kinase mediated events;Cell Cycle Checkpoints;RHO GTPases activate PKNs;Cyclin A/B1/B2 associated events during G2/M transition;RHO GTPase Effectors;Signaling by Rho GTPases;TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest;TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain;TP53 Regulates Transcription of Cell Cycle Genes;G2/M Transition;Mitotic G2-G2/M phases;Transcriptional Regulation by TP53;Cell Cycle;Cell Cycle, Mitotic;PLK3 signaling events;PLK1 signaling events;ATM pathway;ATR signaling pathway (Consensus)

Recessive Scores

• pRec: 0.420

Intolerance Scores

• loftool: 0.971
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.09

Haploinsufficiency Scores

• pHI: 0.988
• hipred: Y
• hipred_score: 0.566
• ghis: 0.611

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000611

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cdc25c
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular 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; digestive/alimentary phenotype

Gene ontology

• 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;cell population proliferation;positive regulation of G2/M transition of mitotic cell cycle;viral process;peptidyl-tyrosine dephosphorylation;positive regulation of mitotic cell cycle;cell division;positive regulation of G2/MI transition of meiotic cell cycle
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;nuclear speck;perinuclear region of cytoplasm
• Molecular function: phosphoprotein phosphatase activity;protein tyrosine phosphatase activity;protein binding;protein kinase binding;WW domain binding