CCND3
cyclin D3, the group of Cyclins
Basic information
Region (hg38): 6:41934934-42050357
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 CCND3 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 | |||||
| missense | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 1 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 11 | 0 | 3 |
Variants in CCND3
This is a list of pathogenic ClinVar variants found in the CCND3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-41935995-C-T | not specified | Uncertain significance (Jan 16, 2024) | ||
| 6-41936002-A-G | not specified | Uncertain significance (Apr 22, 2024) | ||
| 6-41936014-C-T | not specified | Uncertain significance (Mar 18, 2024) | ||
| 6-41936074-C-T | not specified | Uncertain significance (Jan 17, 2024) | ||
| 6-41936581-G-A | not specified | Uncertain significance (Jan 16, 2024) | ||
| 6-41936586-C-G | Benign (Dec 31, 2019) | |||
| 6-41937288-C-T | not specified | Uncertain significance (Jun 24, 2022) | ||
| 6-41937349-C-A | not specified | Uncertain significance (Aug 30, 2022) | ||
| 6-41940393-C-T | not specified | Uncertain significance (Jun 22, 2023) | ||
| 6-41940419-T-C | not specified | Uncertain significance (Dec 07, 2021) | ||
| 6-41940512-C-T | not specified | Uncertain significance (May 07, 2024) | ||
| 6-41940531-G-T | not specified | Uncertain significance (Jun 29, 2022) | ||
| 6-41940535-G-A | Benign (Apr 25, 2018) | |||
| 6-41940540-T-C | not specified | Uncertain significance (Jul 11, 2022) | ||
| 6-41941553-G-C | not specified | Uncertain significance (May 31, 2023) | ||
| 6-41941598-C-T | not specified | Uncertain significance (Sep 17, 2021) | ||
| 6-41957421-G-A | Benign (Feb 23, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CCND3 | protein_coding | protein_coding | ENST00000372991 | 5 | 115425 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.983 | 0.0165 | 125745 | 0 | 3 | 125748 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.40 | 114 | 164 | 0.694 | 0.00000847 | 1852 |
| Missense in Polyphen | 35 | 65.295 | 0.53603 | 803 | ||
| Synonymous | 0.0786 | 68 | 68.8 | 0.988 | 0.00000338 | 627 |
| Loss of Function | 3.27 | 0 | 12.5 | 0.00 | 6.25e-7 | 131 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000469 | 0.0000462 |
| European (Non-Finnish) | 0.00000879 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Regulatory component of the cyclin D3-CDK4 (DC) complex that phosphorylates and inhibits members of the retinoblastoma (RB) protein family including RB1 and regulates the cell-cycle during G(1)/S transition. Phosphorylation of RB1 allows dissociation of the transcription factor E2F from the RB/E2F complex and the subsequent transcription of E2F target genes which are responsible for the progression through the G(1) phase. Hypophosphorylates RB1 in early G(1) phase. Cyclin D-CDK4 complexes are major integrators of various mitogenenic and antimitogenic signals. Also substrate for SMAD3, phosphorylating SMAD3 in a cell-cycle-dependent manner and repressing its transcriptional activity. Component of the ternary complex, cyclin D3/CDK4/CDKN1B, required for nuclear translocation and activity of the cyclin D-CDK4 complex. {ECO:0000269|PubMed:15358120}.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Cell cycle - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);p53 signaling pathway - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Measles - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Cell Cycle;miRNA Regulation of DNA Damage Response;miRNAs involved in DNA damage response;Human Thyroid Stimulating Hormone (TSH) signaling pathway;Retinoblastoma (RB) in Cancer;Focal Adhesion;Overview of nanoparticle effects;Wnt Signaling Pathway and Pluripotency;PI3K-Akt Signaling Pathway;Wnt Signaling Pathway;G1 to S cell cycle control;DNA Damage Response;DNA Damage Response (only ATM dependent);Signal Transduction;Gene expression (Transcription);il-2 receptor beta chain in t cell activation;cyclins and cell cycle regulation;Generic Transcription Pathway;MAPK6/MAPK4 signaling;RNA Polymerase II Transcription;Cyclin D associated events in G1;G1 Phase;Mitotic G1-G1/S phases;AndrogenReceptor;Coregulation of Androgen receptor activity;MAPK family signaling cascades;Regulation of RUNX1 Expression and Activity;Cell Cycle;Cell Cycle, Mitotic;Transcriptional regulation by RUNX1;IL2 signaling events mediated by STAT5;Regulation of retinoblastoma protein;E2F transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.467
Intolerance Scores
- loftool
- 0.451
- rvis_EVS
- 0.37
- rvis_percentile_EVS
- 75.12
Haploinsufficiency Scores
- pHI
- 0.883
- hipred
- Y
- hipred_score
- 0.833
- ghis
- 0.502
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.983
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ccnd3
- Phenotype
- normal 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; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); neoplasm; liver/biliary system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; vision/eye phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- regulation of cyclin-dependent protein serine/threonine kinase activity;negative regulation of transcription by RNA polymerase II;mitotic cell cycle;positive regulation of protein phosphorylation;protein phosphorylation;regulation of mitotic nuclear division;signal transduction;positive regulation of cell population proliferation;T cell proliferation;positive regulation of cyclin-dependent protein serine/threonine kinase activity;positive regulation of cell cycle;regulation of insulin receptor signaling pathway;cell division;positive regulation of G1/S transition of mitotic cell cycle
- Cellular component
- cyclin-dependent protein kinase holoenzyme complex;nucleus;nucleoplasm;cytoplasm;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