CDK20

cyclin dependent kinase 20, the group of Cyclin dependent kinases

Basic information

Region (hg38): 9:87966441-87974753

Previous symbols: [ "CCRK" ]

Links

ENSG00000156345 ∙ NCBI:23552 ∙ OMIM:610076 ∙ HGNC:21420 ∙ Uniprot:Q8IZL9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDK20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDK20 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				5	4	9
missense			26	4	1	31
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding				1	8	9
Total	0	0	27	10	13

Variants in CDK20

This is a list of pathogenic ClinVar variants found in the CDK20 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-87967309-G-A			Benign (May 11, 2021)
9-87967465-C-T		CDK20-related disorder	Likely benign (Jan 19, 2018)
9-87967468-C-T		CDK20-related disorder	Likely benign (Nov 08, 2020)
9-87967482-G-A		not specified	Uncertain significance (Feb 01, 2023)
9-87967484-C-T		not specified	Uncertain significance (Jan 24, 2024)
9-87967508-G-A		not specified	Uncertain significance (Jun 09, 2022)
9-87967511-T-G		not specified	Uncertain significance (Jun 24, 2022)
9-87967520-G-C		not specified	Uncertain significance (Apr 23, 2024)
9-87967524-G-A		not specified	Uncertain significance (Jun 10, 2024)
9-87967531-G-A			Likely benign (Sep 28, 2018)
9-87967590-G-A		not specified	Uncertain significance (Apr 24, 2024)
9-87967590-G-C		not specified	Uncertain significance (Nov 14, 2023)
9-87969195-T-C		CDK20-related disorder	Benign (Nov 16, 2019)
9-87969202-C-T		not specified	Uncertain significance (Nov 17, 2022)
9-87969210-C-T		not specified	Uncertain significance (Nov 07, 2022)
9-87969230-A-C		not specified	Likely benign (Jul 11, 2023)
9-87969255-G-T		not specified	Uncertain significance (Dec 28, 2022)
9-87969269-G-A		CDK20-related disorder	Likely benign (Jul 07, 2023)
9-87969280-C-T		not specified	Uncertain significance (Apr 12, 2024)
9-87969282-T-A		not specified	Uncertain significance (Sep 17, 2021)
9-87969284-C-T		not specified	Likely benign (May 15, 2024)
9-87969332-C-CG		Hereditary breast ovarian cancer syndrome	Uncertain significance (Aug 01, 2020)
9-87969333-G-A		not specified	Uncertain significance (May 31, 2023)
9-87969563-C-T			Benign (May 10, 2021)
9-87969810-G-A		not specified	Uncertain significance (May 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDK20	protein_coding	protein_coding	ENST00000325303	8	8313

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.95e-14	0.00814	125672	0	76	125748	0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.940	246	208	1.18	0.0000120	2223
Missense in Polyphen		77	73.951	1.0412		777
Synonymous	-1.38	104	87.6	1.19	0.00000519	715
Loss of Function	-0.505	19	16.8	1.13	8.67e-7	178

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000432	0.000431
Ashkenazi Jewish	0.0000999	0.0000992
East Asian	0.000218	0.000217
Finnish	0.00102	0.00102
European (Non-Finnish)	0.000309	0.000308
Middle Eastern	0.000218	0.000217
South Asian	0.000132	0.000131
Other	0.000494	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for high-level Shh responses in the developing neural tube. Together with TBC1D32, controls the structure of the primary cilium by coordinating assembly of the ciliary membrane and axoneme, allowing GLI2 to be properly activated in response to SHH signaling (By similarity). Involved in cell growth. Activates CDK2, a kinase involved in the control of the cell cycle, by phosphorylating residue 'Thr-160'. {ECO:0000250, ECO:0000269|PubMed:14597612}.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.905
• rvis_EVS: -0.55
• rvis_percentile_EVS: 19.8

Haploinsufficiency Scores

• pHI: 0.185
• hipred: Y
• hipred_score: 0.605
• ghis: 0.562

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdk20
• Phenotype: digestive/alimentary phenotype; limbs/digits/tail 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); vision/eye phenotype; skeleton phenotype; embryo phenotype; pigmentation phenotype; craniofacial phenotype; cellular phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: cdk20
• Affected structure: renal tubule
• Phenotype tag: abnormal
• Phenotype quality: curled

Gene ontology

• Biological process: protein phosphorylation;cell cycle;multicellular organism development;cell division;regulation of cell cycle
• Cellular component: nucleus;nucleoplasm;cytoplasm;cilium
• Molecular function: cyclin-dependent protein serine/threonine kinase activity;protein binding;ATP binding