CDK17

protein-coding

cyclin dependent kinase 17, the group of Cyclin dependent kinases

Gene summary

The protein encoded by this gene belongs to the cdc2/cdkx subfamily of the ser/thr family of protein kinases. It has similarity to a rat protein that is thought to play a role in terminally differentiated neurons. Alternatively spliced transcript variants encoding different isoforms have been found. [provided by RefSeq, Jul 2010]

Previous symbols:

PCTK2

MANE transcript

NM_002595.5

Inheritance

—

ClinVar variants

U:57

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr12:96,278,261-96,400,480

External References & Databases

Ensembl (ENSG00000059758)

Transcript & Mutation Effects

hg38 • Region Span ~122.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CDK17 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 47

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002595.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			50 clinvar			50
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	57	0	0	57

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 50 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002595.5	RefSeq	NP_002586.2	16	MANE Select
ENST00000261211.8	Ensembl	ENSP00000261211.3	16	MANE Select
NM_001170464.4	RefSeq	NP_001163935.1	15	Standard
ENST00000542666.5	Ensembl	ENSP00000442926.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein phosphorylation
regulation of cell cycle

Molecular Function

protein kinase activity
protein serine/threonine kinase activity
cyclin-dependent protein serine/threonine kinase activity
protein binding
ATP binding

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000261211
Coding exons: 16
Length: 122300
Individuals with no LoFs: 125715
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 125742
p: 0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.64	152	275	0.553	0.0000139	3402
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00018	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.000094	0.000092	rare
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.000068	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

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