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.

not_specified (32 variants)

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. These statistics are base on transcript: NM_000001258.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			32 clinvar			32
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	32	0	0

Loading clinvar variants...

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
essential_gene_gene_trap
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