CCNA2

cyclin A2, the group of Cyclins

Basic information

Region (hg38): 4:121816444-121823883

Previous symbols: [ "CCNA", "CCN1" ]

Links

ENSG00000145386 ∙ NCBI:890 ∙ OMIM:123835 ∙ HGNC:1578 ∙ Uniprot:P20248 ∙ 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 CCNA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCNA2 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					2	2
missense			8	2	1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			8	2	3	13
Total	0	0	16	4	6

Variants in CCNA2

This is a list of pathogenic ClinVar variants found in the CCNA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-121816463-T-A			Likely benign (Dec 17, 2022)
4-121816718-A-G			Benign (May 14, 2021)
4-121816759-G-A			Likely benign (Aug 28, 2023)
4-121816810-G-C		EXOSC9-related disorder	Benign (Feb 01, 2024)
4-121816818-C-T		Inborn genetic diseases	Uncertain significance (Jan 04, 2022)
4-121816818-CCAGTGAAAAGAAGAAAAAAGA-C			Uncertain significance (May 10, 2022)
4-121816831-GA-G			Uncertain significance (Mar 23, 2022)
4-121816835-AAAG-A			Uncertain significance (Oct 03, 2021)
4-121816843-G-C			Uncertain significance (Aug 22, 2022)
4-121816846-C-A			Uncertain significance (Mar 04, 2022)
4-121816849-C-T			Uncertain significance (May 31, 2022)
4-121816854-T-G			Uncertain significance (Oct 17, 2022)
4-121818135-G-A		not specified	Uncertain significance (Nov 14, 2023)
4-121818161-C-T		not specified	Likely benign (Oct 25, 2022)
4-121818853-T-C		not specified	Uncertain significance (May 06, 2024)
4-121818891-A-G		not specified	Uncertain significance (Oct 14, 2023)
4-121819566-T-G		not specified	Uncertain significance (Nov 22, 2021)
4-121821037-C-T		not specified	Uncertain significance (Jan 18, 2023)
4-121821062-T-T			Benign (Aug 20, 2018)
4-121822441-G-A		not specified	Uncertain significance (Jun 10, 2024)
4-121822482-C-T			Benign (Jun 14, 2018)
4-121822526-T-C			Benign (Aug 15, 2018)
4-121822532-C-T		not specified	Likely benign (Sep 07, 2022)
4-121822534-T-G		not specified	Uncertain significance (Oct 06, 2021)
4-121822609-T-G		not specified	Uncertain significance (Feb 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CCNA2	protein_coding	protein_coding	ENST00000274026	8	7489

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000379	125731	0	7	125738	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.22	136	231	0.589	0.0000106	2801
Missense in Polyphen		17	58.778	0.28922		774
Synonymous	0.649	82	89.8	0.913	0.00000424	845
Loss of Function	4.41	0	22.6	0.00	0.00000115	274

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000612	0.0000612
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cyclin which controls both the G1/S and the G2/M transition phases of the cell cycle. Functions through the formation of specific serine/threonine protein kinase holoenzyme complexes with the cyclin-dependent protein kinases CDK1 or CDK2. The cyclin subunit confers the substrate specificity of these complexes and differentially interacts with and activates CDK1 and CDK2 throughout the cell cycle. {ECO:0000269|PubMed:1312467}.
• Pathway: Cell cycle - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Hepatitis B - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Progesterone-mediated oocyte maturation - Homo sapiens (human);Cell Cycle;AMP-activated Protein Kinase (AMPK) Signaling;Mitotic G1-G1-S phases;Retinoblastoma (RB) in Cancer;Photodynamic therapy-induced AP-1 survival signaling.;HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA);DNA Repair;Gene expression (Transcription);DNA Double-Strand Break Repair;Generic Transcription Pathway;DNA Damage/Telomere Stress Induced Senescence;Senescence-Associated Secretory Phenotype (SASP);Cellular Senescence;Homology Directed Repair;Cellular responses to stress;Post-translational protein modification;Metabolism of proteins;RNA Polymerase II Transcription;p53-Dependent G1 DNA Damage Response;p53-Dependent G1/S DNA damage checkpoint;G1/S DNA Damage Checkpoints;Cell Cycle Checkpoints;Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1;G0 and Early G1;SCF(Skp2)-mediated degradation of p27/p21;p73 transcription factor network;Cyclin E associated events during G1/S transition ;ATF-2 transcription factor network;Mitotic G1-G1/S phases;Cyclin A:Cdk2-associated events at S phase entry;Orc1 removal from chromatin;DNA Replication;Switching of origins to a post-replicative state;Synthesis of DNA;S Phase;G2 Phase;Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes;Cyclin A/B1/B2 associated events during G2/M transition;Cellular responses to external stimuli;TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest;TP53 Regulates Transcription of Cell Cycle Genes;Ub-specific processing proteases;Regulation of TP53 Degradation;Regulation of TP53 Expression and Degradation;G2/M Transition;Mitotic G2-G2/M phases;Deubiquitination;G1/S Transition;Regulation of TP53 Activity through Phosphorylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Regulation of APC/C activators between G1/S and early anaphase;CDK-mediated phosphorylation and removal of Cdc6;Cdc20:Phospho-APC/C mediated degradation of Cyclin A;APC:Cdc20 mediated degradation of cell cycle proteins prior to satisfation of the cell cycle checkpoint;APC/C:Cdc20 mediated degradation of mitotic proteins;Activation of APC/C and APC/C:Cdc20 mediated degradation of mitotic proteins;APC/C-mediated degradation of cell cycle proteins;Regulation of mitotic cell cycle;Cell Cycle;Cell Cycle, Mitotic;IL2 signaling events mediated by STAT5;Processing of DNA double-strand break ends;FOXM1 transcription factor network;Validated transcriptional targets of AP1 family members Fra1 and Fra2;Regulation of retinoblastoma protein;ATR signaling pathway;E2F transcription factor network;p53 pathway;Signaling events mediated by PRL (Consensus)

Recessive Scores

• pRec: 0.522

Intolerance Scores

• loftool: 0.0958
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.12

Haploinsufficiency Scores

• pHI: 0.999
• hipred: Y
• hipred_score: 0.783
• ghis: 0.602

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.758

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccna2
• Phenotype: immune system phenotype; embryo phenotype; hematopoietic 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

Zebrafish Information Network

• Gene name: ccna2
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: pointed

Gene ontology

• Biological process: regulation of cyclin-dependent protein serine/threonine kinase activity;G2/M transition of mitotic cell cycle;mitotic cell cycle;regulation of DNA replication;regulation of mitotic nuclear division;Ras protein signal transduction;positive regulation of cell population proliferation;viral process;histone phosphorylation;protein deubiquitination;animal organ regeneration;response to glucagon;cellular response to platelet-derived growth factor stimulus;cellular response to leptin stimulus;cell cycle G1/S phase transition;positive regulation of cell cycle;positive regulation of transcription, DNA-templated;positive regulation of fibroblast proliferation;cell division;cellular response to cocaine;cellular response to luteinizing hormone stimulus;cellular response to estradiol stimulus;cellular response to hypoxia;cellular response to nitric oxide;cochlea development;cellular response to insulin-like growth factor stimulus
• Cellular component: cyclin-dependent protein kinase holoenzyme complex;female pronucleus;male pronucleus;nucleus;nucleoplasm;cytoplasm;cytosol;cyclin A2-CDK2 complex
• Molecular function: protein kinase activity;protein binding;cyclin-dependent protein serine/threonine kinase regulator activity;protein kinase binding;protein domain specific binding;cyclin-dependent protein kinase activity