CDC25B

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

Basic information

Region (hg38): 20:3786771-3806121

Links

ENSG00000101224 ∙ NCBI:994 ∙ OMIM:116949 ∙ HGNC:1726 ∙ Uniprot:P30305 ∙ 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 CDC25B gene.

• Inborn genetic diseases (21 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.

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			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	3	0

Variants in CDC25B

This is a list of pathogenic ClinVar variants found in the CDC25B region.

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

Position	Type	Phenotype	Significance	ClinVar
20-3796541-C-T		not specified	Uncertain significance (Aug 02, 2022)
20-3796718-G-A		not specified	Uncertain significance (Dec 16, 2022)
20-3796718-G-T		not specified	Uncertain significance (Jan 18, 2022)
20-3798438-A-G		not specified	Likely benign (Aug 12, 2021)
20-3798450-A-G		not specified	Uncertain significance (Jul 19, 2023)
20-3800482-G-A		not specified	Uncertain significance (May 06, 2022)
20-3800767-G-A		not specified	Uncertain significance (Feb 21, 2024)
20-3800774-G-A		not specified	Uncertain significance (May 26, 2023)
20-3800799-C-T			Likely benign (Oct 01, 2022)
20-3800803-G-A		not specified	Likely benign (Mar 31, 2022)
20-3800975-G-C		not specified	Uncertain significance (Feb 28, 2023)
20-3801260-A-G		not specified	Uncertain significance (May 06, 2022)
20-3801293-A-C		not specified	Uncertain significance (Dec 19, 2022)
20-3801309-G-A		not specified	Uncertain significance (May 15, 2023)
20-3801326-C-T		not specified	Uncertain significance (Apr 07, 2023)
20-3801954-C-T		not specified	Uncertain significance (Feb 28, 2024)
20-3801984-G-A		not specified	Uncertain significance (Aug 15, 2023)
20-3801990-C-T		not specified	Uncertain significance (Sep 26, 2022)
20-3802003-A-G		not specified	Uncertain significance (Jan 04, 2022)
20-3802036-C-T		not specified	Uncertain significance (Dec 22, 2023)
20-3802062-G-A		not specified	Uncertain significance (Jul 21, 2021)
20-3802342-G-A		not specified	Uncertain significance (Jan 23, 2024)
20-3804588-C-G		not specified	Uncertain significance (Jan 29, 2024)
20-3804606-G-A		not specified	Uncertain significance (Jun 24, 2022)
20-3804920-C-T		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

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: dbNSFP

• 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