CCND1
cyclin D1, the group of Cyclins
Basic information
Region (hg38): 11:69641155-69654474
Previous symbols: [ "BCL1", "D11S287E", "PRAD1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (10 variants)
- Inborn genetic diseases (7 variants)
- not specified (1 variants)
- MULTIPLE MYELOMA, t(11;14) TYPE, SUSCEPTIBILITY TO (1 variants)
- VON HIPPEL-LINDAU SYNDROME, MODIFIER OF (1 variants)
- Colorectal cancer, susceptibility to (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCND1 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 | |||||
| missense | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 1 | 1 | ||||
| non coding ? | 6 | |||||
| Total | 0 | 0 | 8 | 3 | 6 |
Variants in CCND1
This is a list of pathogenic ClinVar variants found in the CCND1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 11-69641493-C-G | Likely benign (Aug 08, 2018) | |||
| 11-69643219-CAACTC-GGAG | not specified | Uncertain significance (Aug 23, 2023) | ||
| 11-69643662-G-C | Benign (May 11, 2021) | |||
| 11-69643974-T-C | not specified | Uncertain significance (Aug 12, 2021) | ||
| 11-69643977-C-T | not specified | Uncertain significance (Jul 11, 2023) | ||
| 11-69643986-C-T | not specified | Uncertain significance (Feb 27, 2023) | ||
| 11-69647874-G-A | Benign (May 10, 2021) | |||
| 11-69648068-C-T | CCND1-related disorder | Likely benign (Apr 04, 2019) | ||
| 11-69648088-C-T | CCND1-related disorder | Benign (May 04, 2021) | ||
| 11-69648108-C-T | not specified | Uncertain significance (Oct 14, 2023) | ||
| 11-69648110-C-G | not specified | Uncertain significance (Jun 30, 2022) | ||
| 11-69648133-G-A | CCND1-related disorder | Likely benign (Jul 23, 2019) | ||
| 11-69648142-G-A | Colorectal cancer, susceptibility to • VON HIPPEL-LINDAU SYNDROME, MODIFIER OF • MULTIPLE MYELOMA, t(11;14) TYPE, SUSCEPTIBILITY TO • CCND1-related disorder | Benign (Apr 16, 2020) | ||
| 11-69650913-A-G | Benign (May 10, 2021) | |||
| 11-69651092-A-G | Benign (May 11, 2021) | |||
| 11-69651129-G-A | Benign/Likely benign (Sep 01, 2022) | |||
| 11-69651147-C-G | not specified | Uncertain significance (May 31, 2023) | ||
| 11-69651179-C-T | not specified | Uncertain significance (Jun 24, 2022) | ||
| 11-69651194-A-G | not specified | Uncertain significance (May 04, 2022) | ||
| 11-69651219-AGAG-A | CCND1-related disorder | Likely benign (Sep 15, 2020) | ||
| 11-69651262-G-A | not specified | Uncertain significance (Nov 22, 2022) | ||
| 11-69651347-C-A | Benign (May 10, 2021) | |||
| 11-69652053-C-T | Likely benign (Jan 01, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CCND1 | protein_coding | protein_coding | ENST00000227507 | 5 | 13388 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.891 | 0.109 | 125699 | 0 | 4 | 125703 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.42 | 122 | 175 | 0.698 | 0.00000987 | 1927 |
| Missense in Polyphen | 33 | 67.834 | 0.48648 | 754 | ||
| Synonymous | -1.12 | 91 | 78.3 | 1.16 | 0.00000485 | 578 |
| Loss of Function | 2.88 | 1 | 11.6 | 0.0864 | 4.93e-7 | 136 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000265 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Regulatory component of the cyclin D1-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 D1/CDK4/CDKN1B, required for nuclear translocation and activity of the cyclin D-CDK4 complex. Exhibits transcriptional corepressor activity with INSM1 on the NEUROD1 and INS promoters in a cell cycle-independent manner. {ECO:0000269|PubMed:15241418, ECO:0000269|PubMed:16569215, ECO:0000269|PubMed:18417529, ECO:0000269|PubMed:9106657}.;
- Disease
- DISEASE: Note=A chromosomal aberration involving CCND1 may be a cause of B-lymphocytic malignancy, particularly mantle-cell lymphoma (MCL). Translocation t(11;14)(q13;q32) with immunoglobulin gene regions. Activation of CCND1 may be oncogenic by directly altering progression through the cell cycle.; DISEASE: Note=A chromosomal aberration involving CCND1 may be a cause of parathyroid adenomas. Translocation t(11;11)(q13;p15) with the parathyroid hormone (PTH) enhancer.; DISEASE: Multiple myeloma (MM) [MIM:254500]: A malignant tumor of plasma cells usually arising in the bone marrow and characterized by diffuse involvement of the skeletal system, hyperglobulinemia, Bence-Jones proteinuria and anemia. Complications of multiple myeloma are bone pain, hypercalcemia, renal failure and spinal cord compression. The aberrant antibodies that are produced lead to impaired humoral immunity and patients have a high prevalence of infection. Amyloidosis may develop in some patients. Multiple myeloma is part of a spectrum of diseases ranging from monoclonal gammopathy of unknown significance (MGUS) to plasma cell leukemia. {ECO:0000269|PubMed:8695815}. Note=The gene represented in this entry is involved in disease pathogenesis. A chromosomal aberration involving CCND1 is found in multiple myeloma. Translocation t(11;14)(q13;q32) with the IgH locus.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Non-small cell lung cancer - Homo sapiens (human);Chronic myeloid leukemia - Homo sapiens (human);Gastric cancer - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Oxytocin signaling pathway - Homo sapiens (human);Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Melanoma - Homo sapiens (human);AGE-RAGE signaling pathway in diabetic complications - Homo sapiens (human);Cushing,s syndrome - Homo sapiens (human);Bladder cancer - Homo sapiens (human);Cell cycle - Homo sapiens (human);Viral myocarditis - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);p53 signaling pathway - Homo sapiens (human);Tight junction - Homo sapiens (human);Small cell lung cancer - Homo sapiens (human);Acute myeloid leukemia - Homo sapiens (human);Breast cancer - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Glioma - Homo sapiens (human);Thyroid hormone signaling pathway - Homo sapiens (human);Prostate cancer - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Apelin signaling pathway - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Prolactin signaling pathway - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Hepatitis B - Homo sapiens (human);Measles - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Thyroid cancer - Homo sapiens (human);Pancreatic cancer - Homo sapiens (human);Endometrial cancer - Homo sapiens (human);Colorectal cancer - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Hedgehog signaling pathway - Homo sapiens (human);Androgen receptor signaling pathway;miRNA Regulation of DNA Damage Response;miRNAs involved in DNA damage response;miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Leptin signaling pathway;IL-7 Signaling Pathway;Signaling Pathways in Glioblastoma;Spinal Cord Injury;Retinoblastoma (RB) in Cancer;Integrated Lung Cancer Pathway;Polycystic Kidney Disease Pathway;JAK-STAT;Bladder Cancer;Mesodermal Commitment Pathway;Vitamin D Receptor Pathway;PPAR Alpha Pathway;Nuclear Receptors Meta-Pathway;Focal Adhesion;Copper homeostasis;Photodynamic therapy-induced AP-1 survival signaling.;Photodynamic therapy-induced NF-kB survival signaling;Wnt Signaling Pathway;Hepatitis C and Hepatocellular Carcinoma;TGF-beta Signaling Pathway;VEGFA-VEGFR2 Signaling Pathway;H19 action Rb-E2F1 signaling and CDK-β-catenin activity;miRNA regulation of prostate cancer signaling pathways;Wnt Signaling Pathway and Pluripotency;Interleukin-4 and 13 signaling;Transcriptional regulation by RUNX3;Endometrial cancer;PI3K-Akt Signaling Pathway;Chromosomal and microsatellite instability in colorectal cancer;Hedgehog Signaling Pathway;Wnt Signaling Pathway;G1 to S cell cycle control;Notch Signaling Pathway;ErbB Signaling Pathway;DNA Damage Response;DNA Damage Response (only ATM dependent);Signaling by PTK6;RAGE;Transcriptional regulation by RUNX2;Signal Transduction;Gene expression (Transcription);RUNX3 regulates WNT signaling;RUNX3 regulates p14-ARF;Transcriptional regulation by RUNX3;btg family proteins and cell cycle regulation;influence of ras and rho proteins on g1 to s transition;wnt signaling pathway;il-2 receptor beta chain in t cell activation;cell cycle: g1/s check point;cyclins and cell cycle regulation;Generic Transcription Pathway;Prolactin;RNA Polymerase II Transcription;RMTs methylate histone arginines;Chromatin modifying enzymes;Cyclin D associated events in G1;G1 Phase;SCF(Skp2)-mediated degradation of p27/p21;Cyclin E associated events during G1/S transition ;ATF-2 transcription factor network;Pre-NOTCH Transcription and Translation;Pre-NOTCH Expression and Processing;PTK6 Regulates Cell Cycle;inactivation of gsk3 by akt causes accumulation of b-catenin in alveolar macrophages;Mitotic G1-G1/S phases;Cyclin A:Cdk2-associated events at S phase entry;Signaling by NOTCH;AndrogenReceptor;Ubiquitin-dependent degradation of Cyclin D1;Ubiquitin-dependent degradation of Cyclin D;S Phase;p53 signaling pathway;TGF_beta_Receptor;Coregulation of Androgen receptor activity;Signaling by Non-Receptor Tyrosine Kinases;G1/S Transition;Signaling by Nuclear Receptors;Chromatin organization;C-MYB transcription factor network;Notch signaling pathway;Regulation of RUNX1 Expression and Activity;Estrogen-dependent gene expression;Cell Cycle;Wnt;Integrin-linked kinase signaling;Cell Cycle, Mitotic;ESR-mediated signaling;Regulation of nuclear beta catenin signaling and target gene transcription;Transcriptional regulation by RUNX1;Neurotrophic factor-mediated Trk receptor signaling;Validated nuclear estrogen receptor alpha network;Validated targets of C-MYC transcriptional repression;Regulation of Telomerase;Signaling events mediated by focal adhesion kinase;AP-1 transcription factor network;FOXM1 transcription factor network;Trk receptor signaling mediated by PI3K and PLC-gamma;Validated transcriptional targets of AP1 family members Fra1 and Fra2;Regulation of retinoblastoma protein;Presenilin action in Notch and Wnt signaling;Signaling mediated by p38-gamma and p38-delta;E-cadherin signaling in the nascent adherens junction
(Consensus)
Recessive Scores
- pRec
- 0.963
Intolerance Scores
- loftool
- 0.189
- rvis_EVS
- -0.32
- rvis_percentile_EVS
- 31.46
Haploinsufficiency Scores
- pHI
- 0.999
- hipred
- Y
- hipred_score
- 0.831
- ghis
- 0.509
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.999
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ccnd1
- Phenotype
- craniofacial phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland 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); hematopoietic system phenotype; growth/size/body region phenotype; reproductive system phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); 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); vision/eye phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; immune system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); neoplasm;
Zebrafish Information Network
- Gene name
- ccnd1
- Affected structure
- retinal inner plexiform layer
- Phenotype tag
- abnormal
- Phenotype quality
- decreased thickness
Gene ontology
- Biological process
- regulation of cyclin-dependent protein serine/threonine kinase activity;G1/S transition of mitotic cell cycle;negative regulation of transcription by RNA polymerase II;mitotic cell cycle;re-entry into mitotic cell cycle;positive regulation of protein phosphorylation;transcription initiation from RNA polymerase II promoter;protein phosphorylation;cellular response to DNA damage stimulus;regulation of mitotic nuclear division;lactation;positive regulation of cell population proliferation;response to iron ion;response to X-ray;response to organonitrogen compound;positive regulation of G2/M transition of mitotic cell cycle;Wnt signaling pathway;cytokine-mediated signaling pathway;negative regulation of epithelial cell differentiation;endoplasmic reticulum unfolded protein response;mitotic G1 DNA damage checkpoint;response to magnesium ion;response to estradiol;response to vitamin E;Leydig cell differentiation;mammary gland epithelial cell proliferation;positive regulation of mammary gland epithelial cell proliferation;response to drug;response to estrogen;response to leptin;fat cell differentiation;response to ethanol;positive regulation of cyclin-dependent protein serine/threonine kinase activity;positive regulation of cell cycle;cell division;response to corticosterone;response to calcium ion;mammary gland alveolus development;response to UV-A;negative regulation of cell cycle arrest;liver regeneration;positive regulation of G1/S transition of mitotic cell cycle
- Cellular component
- cyclin-dependent protein kinase holoenzyme complex;nucleus;nucleoplasm;cytoplasm;cytosol;bicellular tight junction;membrane;transcriptional repressor complex
- Molecular function
- transcription corepressor activity;protein kinase activity;cyclin-dependent protein serine/threonine kinase activity;protein binding;transcription factor binding;cyclin-dependent protein serine/threonine kinase regulator activity;enzyme binding;protein kinase binding;histone deacetylase binding;protein-containing complex binding;proline-rich region binding