CCND3

cyclin D3, the group of Cyclins

Basic information

Region (hg38): 6:41934933-42050357

Links

ENSG00000112576 ∙ NCBI:896 ∙ OMIM:123834 ∙ HGNC:1585 ∙ Uniprot:P30281 ∙ 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 CCND3 gene.

• Inborn genetic diseases (8 variants)
• not provided (3 variants)

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	2
missense			7			7
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	8	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)
6-41936074-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)
6-41940531-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: gnomAD

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: dbNSFP

• 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