CDK3

cyclin dependent kinase 3, the group of Cyclin dependent kinases

Basic information

Region (hg38): 17:76000855-76005999

Links

ENSG00000250506 ∙ NCBI:1018 ∙ OMIM:123828 ∙ HGNC:1772 ∙ Uniprot:Q00526 ∙ 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 CDK3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDK3 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						0
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in CDK3

This is a list of pathogenic ClinVar variants found in the CDK3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-76002046-G-C		not specified	Uncertain significance (Mar 31, 2024)
17-76002053-C-A		not specified	Uncertain significance (Nov 17, 2023)
17-76002111-C-G		not specified	Uncertain significance (Apr 17, 2024)
17-76002252-A-G		not specified	Uncertain significance (Nov 02, 2023)
17-76002254-C-G		not specified	Uncertain significance (Jul 25, 2023)
17-76002294-A-G		not specified	Uncertain significance (Mar 28, 2024)
17-76002303-T-C		not specified	Uncertain significance (Apr 17, 2024)
17-76002309-G-A		not specified	Uncertain significance (Oct 25, 2022)
17-76002323-C-A		not specified	Uncertain significance (Aug 11, 2024)
17-76002381-G-A		not specified	Uncertain significance (Oct 11, 2024)
17-76002392-G-A		not specified	Uncertain significance (Jan 03, 2024)
17-76002395-C-T		not specified	Uncertain significance (Aug 12, 2024)
17-76002566-C-A		not specified	Uncertain significance (Aug 12, 2021)
17-76003246-C-T		not specified	Uncertain significance (Apr 09, 2024)
17-76005298-C-G		not specified	Uncertain significance (Feb 27, 2024)
17-76005350-C-A		not specified	Uncertain significance (Nov 25, 2024)
17-76005410-G-A		not specified	Uncertain significance (Apr 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDK3	protein_coding	protein_coding	ENST00000425876	7	5094

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.14e-7	0.468	125668	0	80	125748	0.000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.628	158	182	0.869	0.0000104	1972
Missense in Polyphen		71	85.711	0.82837		918
Synonymous	-1.27	91	76.8	1.18	0.00000441	622
Loss of Function	0.810	12	15.4	0.778	8.95e-7	161

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000235	0.000235
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00208	0.00208
European (Non-Finnish)	0.000194	0.000167
Middle Eastern	0.000109	0.000109
South Asian	0.000229	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine/threonine-protein kinase that plays a critical role in the control of the eukaryotic cell cycle; involved in G0- G1 and G1-S cell cycle transitions. Interacts with CCNC/cyclin-C during interphase. Phosphorylates histone H1, ATF1, RB1 and CABLES1. ATF1 phosphorylation triggers ATF1 transactivation and transcriptional activities, and promotes cell proliferation and transformation. CDK3/cyclin-C mediated RB1 phosphorylation is required for G0-G1 transition. Promotes G1-S transition probably by contributing to the activation of E2F1, E2F2 and E2F3 in a RB1- independent manner. {ECO:0000269|PubMed:15084261, ECO:0000269|PubMed:18794154, ECO:0000269|PubMed:8846921}.
• Pathway: estrogen responsive protein efp controls cell cycle and breast tumors growth;IL-7 signaling;JAK STAT pathway and regulation;EPO signaling;VEGF (Consensus)

Recessive Scores

• pRec: 0.208

Intolerance Scores

• loftool: 0.668
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• pHI: 0.968
• hipred: N
• hipred_score: 0.350
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.989

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdk3-ps
• Phenotype: normal phenotype

Gene ontology

• Biological process: G1/S transition of mitotic cell cycle;protein phosphorylation;cellular response to DNA damage stimulus;cell population proliferation;G0 to G1 transition;cell division;regulation of cell cycle
• Cellular component: nucleus
• Molecular function: cyclin-dependent protein serine/threonine kinase activity;protein binding;ATP binding