CCNA1
cyclin A1, the group of Cyclins
Basic information
Region (hg38): 13:36431520-36442870
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCNA1 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 | 5 | |||||
| missense | 15 | 16 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 6 | |||||
| Total | 0 | 0 | 21 | 3 | 3 |
Variants in CCNA1
This is a list of pathogenic ClinVar variants found in the CCNA1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 13-36432653-C-G | not specified | Uncertain significance (Nov 07, 2022) | ||
| 13-36432671-G-A | not specified | Uncertain significance (Sep 14, 2021) | ||
| 13-36432679-G-A | not specified | Uncertain significance (Mar 06, 2023) | ||
| 13-36432686-A-G | not specified | Uncertain significance (Jan 18, 2022) | ||
| 13-36432701-G-A | not specified | Uncertain significance (Aug 28, 2023) | ||
| 13-36432704-C-T | not specified | Uncertain significance (Apr 25, 2023) | ||
| 13-36433038-G-C | not specified | Uncertain significance (Jun 22, 2024) | ||
| 13-36433067-G-T | not specified | Uncertain significance (Jun 10, 2024) | ||
| 13-36433096-A-G | not specified | Uncertain significance (Dec 20, 2023) | ||
| 13-36433102-G-A | not specified | Uncertain significance (Sep 21, 2023) | ||
| 13-36433204-A-G | not specified | Uncertain significance (Jun 04, 2024) | ||
| 13-36437652-T-C | Benign (Dec 31, 2019) | |||
| 13-36437665-A-G | not specified | Uncertain significance (Dec 06, 2023) | ||
| 13-36437722-C-T | not specified | Uncertain significance (Aug 12, 2021) | ||
| 13-36437732-G-A | not specified | Uncertain significance (Mar 19, 2024) | ||
| 13-36437775-C-G | not specified | Uncertain significance (Jan 22, 2024) | ||
| 13-36437795-G-T | not specified | Uncertain significance (Apr 24, 2024) | ||
| 13-36437830-G-A | not specified | Likely benign (Jun 28, 2022) | ||
| 13-36437880-C-A | Benign (Dec 31, 2019) | |||
| 13-36438089-A-G | Likely benign (Jun 08, 2018) | |||
| 13-36438093-C-G | not specified | Uncertain significance (May 25, 2022) | ||
| 13-36438154-A-G | not specified | Uncertain significance (Nov 21, 2023) | ||
| 13-36438689-A-G | not specified | Uncertain significance (Nov 08, 2022) | ||
| 13-36438694-G-A | Benign (Jun 06, 2018) | |||
| 13-36438717-T-G | not specified | Uncertain significance (Feb 03, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CCNA1 | protein_coding | protein_coding | ENST00000255465 | 9 | 11053 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000431 | 0.998 | 125733 | 0 | 15 | 125748 | 0.0000596 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.25 | 193 | 248 | 0.777 | 0.0000121 | 3001 |
| Missense in Polyphen | 55 | 95.859 | 0.57376 | 1227 | ||
| Synonymous | -0.461 | 104 | 98.2 | 1.06 | 0.00000498 | 938 |
| Loss of Function | 2.77 | 10 | 24.9 | 0.401 | 0.00000148 | 268 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000123 | 0.000123 |
| Ashkenazi Jewish | 0.000200 | 0.000198 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.0000924 | 0.0000924 |
| European (Non-Finnish) | 0.0000440 | 0.0000439 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.0000654 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in the control of the cell cycle at the G1/S (start) and G2/M (mitosis) transitions. May primarily function in the control of the germline meiotic cell cycle and additionally in the control of mitotic cell cycle in some somatic cells. {ECO:0000269|PubMed:10022926}.;
- Pathway
- Cell cycle - Homo sapiens (human);Acute myeloid leukemia - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Transcriptional misregulation in cancer - 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;Gastric Cancer Network 1;G1 to S cell cycle control;HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA);DNA Repair;Gene expression (Transcription);DNA Double-Strand Break Repair;il-2 receptor beta chain in t cell activation;cell cycle: g1/s check point;cyclins and cell cycle regulation;e2f1 destruction pathway;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;G0 and Early G1;SCF(Skp2)-mediated degradation of p27/p21;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;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;C-MYB transcription factor network;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;Processing of DNA double-strand break ends
(Consensus)
Recessive Scores
- pRec
- 0.386
Intolerance Scores
- loftool
- 0.833
- rvis_EVS
- -0.49
- rvis_percentile_EVS
- 22.36
Haploinsufficiency Scores
- pHI
- 0.737
- hipred
- Y
- hipred_score
- 0.734
- ghis
- 0.466
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.437
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ccna1
- Phenotype
- cellular phenotype; endocrine/exocrine gland phenotype; immune system 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); reproductive system phenotype;
Gene ontology
- Biological process
- regulation of cyclin-dependent protein serine/threonine kinase activity;regulation of transcription involved in G1/S transition of mitotic cell cycle;mitotic cell cycle;protein phosphorylation;regulation of mitotic nuclear division;male meiosis I;spermatogenesis;positive regulation of cell population proliferation;protein deubiquitination;positive regulation of cell cycle;cell division
- Cellular component
- cyclin-dependent protein kinase holoenzyme complex;nucleus;nucleoplasm;cytoplasm;cytosol;microtubule cytoskeleton;cyclin A1-CDK2 complex;cyclin A2-CDK2 complex
- Molecular function
- protein kinase activity;protein binding;cyclin-dependent protein serine/threonine kinase regulator activity;protein kinase binding