CDC25A

cell division cycle 25A, the group of Class III Cys-based CDC25 phosphatases

Basic information

Region (hg38): 3:48157146-48188417

Links

ENSG00000164045 ∙ NCBI:993 ∙ OMIM:116947 ∙ HGNC:1725 ∙ Uniprot:P30304 ∙ 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 CDC25A gene.

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.

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			24	3	1	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	3	1

Variants in CDC25A

This is a list of pathogenic ClinVar variants found in the CDC25A region.

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

Position	Type	Phenotype	Significance	ClinVar
3-48159408-T-C		not specified	Uncertain significance (May 27, 2022)
3-48164353-T-C		not specified	Uncertain significance (Sep 27, 2024)
3-48164371-T-C		not specified	Uncertain significance (May 16, 2024)
3-48165653-C-T		not specified	Uncertain significance (Oct 03, 2022)
3-48165703-T-C		Autosomal dominant polycystic liver disease • not specified	Uncertain significance (Mar 29, 2022)
3-48165877-G-A		Autosomal dominant polycystic liver disease • not specified	Uncertain significance (Aug 21, 2024)
3-48167872-T-C		not specified	Uncertain significance (Mar 31, 2023)
3-48167880-T-C		not specified	Likely benign (Jun 12, 2023)
3-48167907-T-C		Autosomal dominant polycystic liver disease	Likely benign (Sep 01, 2021)
3-48167910-G-C		not specified	Uncertain significance (Oct 17, 2023)
3-48167922-A-G		not specified	Likely benign (May 25, 2022)
3-48167941-G-C		not specified	Uncertain significance (Nov 13, 2023)
3-48174307-T-C		not specified	Likely benign (Jul 25, 2023)
3-48174312-T-A		not specified	Uncertain significance (Oct 12, 2021)
3-48174405-C-T		not specified	Uncertain significance (Nov 29, 2023)
3-48174415-A-T		not specified	Uncertain significance (May 26, 2024)
3-48174446-G-C		not specified	Uncertain significance (Aug 09, 2021)
3-48177391-C-T		not specified	Uncertain significance (Aug 01, 2024)
3-48177860-A-C		not specified	Uncertain significance (Sep 22, 2023)
3-48177870-T-A		not specified	Uncertain significance (Sep 12, 2023)
3-48177883-C-T		not specified	Likely benign (May 02, 2024)
3-48177933-G-T		not specified	Uncertain significance (Jun 12, 2023)
3-48180725-C-A		not specified	Uncertain significance (Oct 05, 2023)
3-48180791-A-C		not specified	Uncertain significance (Jan 29, 2024)
3-48180800-C-T		not specified	Uncertain significance (Jul 26, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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