CCNB3

cyclin B3, the group of Cyclins

Basic information

Region (hg38): X:50202713-50351914

Links

ENSG00000147082 ∙ NCBI:85417 ∙ OMIM:300456 ∙ HGNC:18709 ∙ Uniprot:Q8WWL7 ∙ 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 CCNB3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCNB3 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				6	3	9
missense			51	9	2	62
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	51	15	5

Variants in CCNB3

This is a list of pathogenic ClinVar variants found in the CCNB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-50288799-C-G		not specified	Uncertain significance (Dec 20, 2023)
X-50288807-T-C		not specified	Uncertain significance (Jun 29, 2023)
X-50288823-A-G		not specified	Uncertain significance (Nov 03, 2023)
X-50294913-T-C			Likely benign (Sep 01, 2022)
X-50294948-C-T		not specified	Uncertain significance (Sep 16, 2021)
X-50308530-G-C		not specified	Uncertain significance (Jun 18, 2024)
X-50308545-G-A		not specified	Likely benign (Nov 19, 2022)
X-50308660-C-T		not specified	Uncertain significance (Apr 29, 2024)
X-50308666-T-C		not specified	Likely benign (Apr 07, 2022)
X-50308731-T-A			Benign (Jul 23, 2018)
X-50308752-C-T		not specified	Likely benign (Aug 28, 2023)
X-50308839-A-G		not specified	Uncertain significance (Apr 19, 2023)
X-50308857-T-C		not specified	Uncertain significance (May 14, 2024)
X-50308876-G-A		not specified	Uncertain significance (Jul 19, 2023)
X-50308913-G-A			Likely benign (Apr 01, 2022)
X-50308926-G-C		not specified	Uncertain significance (Nov 15, 2023)
X-50308934-T-C			Benign (Jun 04, 2018)
X-50308959-G-A		not specified	Uncertain significance (Mar 20, 2024)
X-50308969-G-A		not specified	Likely benign (Mar 02, 2023)
X-50309002-T-C		not specified	Likely benign (Feb 12, 2024)
X-50309062-A-G		not specified	Conflicting classifications of pathogenicity (Sep 01, 2021)
X-50309140-A-G		not specified	Uncertain significance (Jun 22, 2021)
X-50309253-C-T		not specified	Uncertain significance (Sep 14, 2021)
X-50309392-C-G		not specified	Uncertain significance (Jul 14, 2023)
X-50309399-G-T		not specified	Uncertain significance (Jun 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCNB3	protein_coding	protein_coding	ENST00000376042	11	127546

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.859	0.141	125388	2	2	125392	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.840	429	481	0.892	0.0000333	9223
Missense in Polyphen		39	81.757	0.47702		1757
Synonymous	1.33	169	192	0.878	0.0000138	2608
Loss of Function	4.34	6	32.8	0.183	0.00000230	736

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000795	0.0000545
Finnish	0.0000732	0.0000464
European (Non-Finnish)	0.0000251	0.0000176
Middle Eastern	0.0000795	0.0000545
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cyclins are positive regulatory subunits of the cyclin- dependent kinases (CDKs), and thereby play an essential role in the control of the cell cycle, notably via their destruction during cell division. Its tissue specificity suggest that it may be required during early meiotic prophase I. {ECO:0000269|PubMed:12185076}.
• Pathway: Cell cycle - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Progesterone-mediated oocyte maturation - Homo sapiens (human);Cell Cycle;miRNA Regulation of DNA Damage Response;DNA Damage Response (Consensus)

Intolerance Scores

• loftool: 0.418
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.6

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.465

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccnb3

Gene ontology

• Biological process: regulation of cyclin-dependent protein serine/threonine kinase activity;mitotic cell cycle;protein phosphorylation;regulation of mitotic nuclear division;positive regulation of cell population proliferation;regulation of G2/M transition of mitotic cell cycle;positive regulation of cell cycle;cell division;meiotic cell cycle
• Cellular component: cyclin-dependent protein kinase holoenzyme complex;nucleus;cytoplasm;centrosome;nuclear speck
• Molecular function: protein kinase activity;protein binding;cyclin-dependent protein serine/threonine kinase regulator activity;protein kinase binding