CCNB2

cyclin B2, the group of Cyclins

Basic information

Region (hg38): 15:59105126-59125045

Links

ENSG00000157456 ∙ NCBI:9133 ∙ OMIM:602755 ∙ HGNC:1580 ∙ Uniprot:O95067 ∙ 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 CCNB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCNB2 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				3		3
missense			20	1	2	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	20	4	2

Variants in CCNB2

This is a list of pathogenic ClinVar variants found in the CCNB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-59107350-C-T		not specified	Uncertain significance (Mar 26, 2024)
15-59107573-A-T		not specified	Uncertain significance (Dec 21, 2023)
15-59107610-C-G		not specified	Uncertain significance (Aug 08, 2023)
15-59107642-C-T		not specified	Uncertain significance (Nov 03, 2022)
15-59107670-G-A			Benign (Jun 26, 2018)
15-59114461-T-G			Likely benign (Jul 05, 2018)
15-59114475-T-C			Benign (Jul 13, 2018)
15-59114592-A-G		not specified	Uncertain significance (Nov 30, 2022)
15-59114740-A-G		not specified	Uncertain significance (Mar 23, 2023)
15-59114760-A-G		not specified	Uncertain significance (Aug 12, 2021)
15-59114769-C-T		not specified	Uncertain significance (Aug 12, 2021)
15-59114770-G-A		not specified	Uncertain significance (Mar 19, 2024)
15-59114774-G-A		not specified	Uncertain significance (Feb 01, 2023)
15-59114788-T-C		not specified	Uncertain significance (Dec 15, 2022)
15-59114831-G-C		not specified	Uncertain significance (Dec 12, 2023)
15-59114866-G-A		not specified	Uncertain significance (Oct 22, 2021)
15-59116696-C-A		not specified	Uncertain significance (Apr 13, 2022)
15-59116705-C-T		not specified	Uncertain significance (Nov 04, 2023)
15-59116746-G-C		not specified	Uncertain significance (Nov 18, 2021)
15-59116787-A-C		not specified	Uncertain significance (Dec 02, 2022)
15-59116837-A-G		not specified	Uncertain significance (Mar 17, 2023)
15-59116871-A-C		not specified	Uncertain significance (Jun 05, 2024)
15-59116914-A-G			Likely benign (Jul 01, 2022)
15-59117269-G-C		not specified	Uncertain significance (Dec 13, 2022)
15-59117281-C-T		not specified	Likely benign (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCNB2	protein_coding	protein_coding	ENST00000288207	9	19968

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.74e-12	0.211	125713	0	33	125746	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0714	207	210	0.986	0.0000104	2599
Missense in Polyphen		64	72.115	0.88747		934
Synonymous	-0.744	84	75.8	1.11	0.00000384	750
Loss of Function	0.875	20	24.7	0.810	0.00000153	259

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000295	0.000294
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.000218	0.000217
South Asian	0.000164	0.000163
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential for the control of the cell cycle at the G2/M (mitosis) transition.
• Pathway: Cell cycle - Homo sapiens (human);Oocyte meiosis - Homo sapiens (human);p53 signaling pathway - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Progesterone-mediated oocyte maturation - Homo sapiens (human);Cell Cycle;miRNA Regulation of DNA Damage Response;Mitotic G2-G2-M phases;Retinoblastoma (RB) in Cancer;TGF-beta Signaling Pathway;DNA Damage Response;estrogen responsive protein efp controls cell cycle and breast tumors growth;G2/M DNA replication checkpoint;G2/M Checkpoints;Polo-like kinase mediated events;Cell Cycle Checkpoints;Cyclin A/B1/B2 associated events during G2/M transition;Nuclear Pore Complex (NPC) Disassembly;TGF_beta_Receptor;Regulation of PLK1 Activity at G2/M Transition;Golgi Cisternae Pericentriolar Stack Reorganization;The role of GTSE1 in G2/M progression after G2 checkpoint;G2/M Transition;Mitotic G2-G2/M phases;Activation of NIMA Kinases NEK9, NEK6, NEK7;Nuclear Envelope Breakdown;Mitotic Prophase;Condensation of Prometaphase Chromosomes;Mitotic Prometaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic;Validated transcriptional targets of deltaNp63 isoforms;FOXM1 transcription factor network (Consensus)

Recessive Scores

• pRec: 0.177

Intolerance Scores

• loftool: 0.842
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.36

Haploinsufficiency Scores

• pHI: 0.869
• hipred: Y
• hipred_score: 0.515
• ghis: 0.615

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.474

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccnb2
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; immune system 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); hematopoietic system phenotype

Gene ontology

• Biological process: regulation of cyclin-dependent protein serine/threonine kinase activity;G2/M transition of mitotic cell cycle;mitotic cell cycle;in utero embryonic development;protein phosphorylation;mitotic nuclear envelope disassembly;regulation of mitotic nuclear division;positive regulation of cell population proliferation;regulation of growth;T cell homeostasis;positive regulation of cell cycle;thymus development;cell division;regulation of cell cycle
• Cellular component: cyclin-dependent protein kinase holoenzyme complex;nucleus;cytoplasm;centrosome;cytosol;microtubule cytoskeleton;membrane
• Molecular function: protein kinase activity;cyclin-dependent protein serine/threonine kinase activity;protein binding;cyclin-dependent protein serine/threonine kinase regulator activity;protein kinase binding;cadherin binding