CDK15

protein-coding

cyclin dependent kinase 15, the group of Cyclin dependent kinases

Gene summary

Enables protein serine/threonine kinase activity. Predicted to be involved in regulation of cell cycle phase transition. Predicted to be part of cyclin-dependent protein kinase holoenzyme complex. Predicted to be active in cytosol and nucleus. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ALS2CR7
PFTK2

MANE transcript

NM_001366386.2

Inheritance

—

ClinVar variants

U:58

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.97

Max pathogenic AF

—

Genomic locus

chr2:201,790,461-201,895,550

External References & Databases

Ensembl (ENSG00000138395)

Transcript & Mutation Effects

hg38 • Region Span ~105.1 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 CDK15 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 56

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001366386.2. 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			1 clinvar			1
missense			57 clinvar			57
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	58	0	0	58

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001366386.2	RefSeq	NP_001353315.1	13	MANE Select
ENST00000652192.3	Ensembl	ENSP00000498608.2	13	MANE Select
NM_001261435.1	RefSeq	NP_001248364.1	13	Standard
NM_001261436.1	RefSeq	NP_001248365.1	13	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 serine/threonine kinase activity
cyclin-dependent protein serine/threonine kinase activity
protein binding
ATP binding
cyclin binding

Cellular Component

nucleus
cytoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000450471
Coding exons: 13
Length: 105090
Individuals with no LoFs: 125277
Homozygous LoFs: 2
Heterozygous LoFs: 469
Defined: 125748
p: 0.00187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.00459	239	239	1.00	0.0000126	2794
Missense (PolyPhen)		79	84.184	0.93843		972
Synonymous	-0.364	96	91.6	1.05	0.00000495	834
Loss of Function	0.126	26	26.7	0.974	0.00000129	304

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0051	0.0050	notable
Latino/Admixed American	0.0018	0.0018	notable
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.0010	0.0010	notable
Finnish	0.0024	0.0025	notable
European (Non-Finnish)	0.0017	0.0017	notable
South Asian	0.0019	0.0019	notable
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Serine/threonine-protein kinase that acts like an antiapoptotic protein that counters TRAIL/TNFSF10-induced apoptosis by inducing phosphorylation of BIRC5 at 'Thr-34'. {ECO:0000269|PubMed:24866247}.;

Recessive Scores

pRec: 0.0829

Intolerance Scores

LoFtool: 0.940
RVIS EVS: -0.02
RVIS percentile EVS: 52.09

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