CDK17

cyclin dependent kinase 17, the group of Cyclin dependent kinases

Basic information

Region (hg38): 12:96278261-96400480

Previous symbols: [ "PCTK2" ]

Links

ENSG00000059758 ∙ NCBI:5128 ∙ OMIM:603440 ∙ HGNC:8750 ∙ Uniprot:Q00537 ∙ 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 CDK17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDK17 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			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	27	0	0

Variants in CDK17

This is a list of pathogenic ClinVar variants found in the CDK17 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-96280831-C-T		not specified	Uncertain significance (Dec 25, 2024)
12-96280837-C-G		not specified	Uncertain significance (Oct 05, 2023)
12-96280840-G-A		not specified	Uncertain significance (Aug 12, 2021)
12-96280877-T-C		not specified	Uncertain significance (Dec 12, 2024)
12-96282544-C-T		not specified	Uncertain significance (Jul 14, 2024)
12-96282589-T-A		not specified	Uncertain significance (Nov 30, 2022)
12-96283605-G-T		not specified	Uncertain significance (Jan 15, 2025)
12-96286083-G-C		not specified	Uncertain significance (Aug 10, 2023)
12-96286125-G-T		not specified	Uncertain significance (Nov 18, 2022)
12-96286702-G-A		not specified	Uncertain significance (Nov 20, 2024)
12-96289192-C-T		not specified	Uncertain significance (Nov 06, 2023)
12-96289194-G-A		not specified	Uncertain significance (Jul 05, 2023)
12-96297275-C-T		not specified	Uncertain significance (Jul 13, 2022)
12-96297281-G-T		not specified	Uncertain significance (Sep 22, 2022)
12-96297313-T-C		not specified	Uncertain significance (Nov 18, 2022)
12-96297646-G-A		not specified	Uncertain significance (Sep 12, 2024)
12-96297725-C-T			Benign (May 30, 2018)
12-96298932-C-G		not specified	Uncertain significance (Jul 19, 2023)
12-96300341-T-C		not specified	Uncertain significance (Oct 26, 2022)
12-96311100-A-T		not specified	Uncertain significance (Nov 13, 2024)
12-96311106-T-C		not specified	Uncertain significance (Jan 18, 2022)
12-96311144-T-G		not specified	Uncertain significance (Nov 07, 2022)
12-96313326-T-C		not specified	Uncertain significance (Mar 02, 2023)
12-96313335-G-A		not specified	Uncertain significance (Nov 18, 2022)
12-96323974-G-A		not specified	Uncertain significance (Sep 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDK17	protein_coding	protein_coding	ENST00000261211	16	122300

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000531	125715	0	27	125742	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.64	152	275	0.553	0.0000139	3402
Missense in Polyphen		47	113.39	0.41449		1404
Synonymous	0.549	86	92.7	0.927	0.00000452	961
Loss of Function	5.01	3	34.9	0.0859	0.00000211	423

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000249	0.000185
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.00	0.00
Finnish	0.0000938	0.0000924
European (Non-Finnish)	0.000170	0.000167
Middle Eastern	0.00	0.00
South Asian	0.0000676	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in terminally differentiated neurons. Has a Ser/Thr-phosphorylating activity for histone H1 (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.615
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.41

Haploinsufficiency Scores

• pHI: 0.209
• hipred: Y
• hipred_score: 0.710
• ghis: 0.676

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdk17

Gene ontology

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