CDK15

cyclin dependent kinase 15, the group of Cyclin dependent kinases

Basic information

Region (hg38): 2:201790461-201895550

Previous symbols: [ "ALS2CR7", "PFTK2" ]

Links

ENSG00000138395 ∙ NCBI:65061 ∙ OMIM:616147 ∙ HGNC:14434 ∙ Uniprot:Q96Q40 ∙ 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 CDK15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDK15 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in CDK15

This is a list of pathogenic ClinVar variants found in the CDK15 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-201807557-G-T		not specified	Uncertain significance (Nov 22, 2021)
2-201807591-G-A		not specified	Uncertain significance (Oct 13, 2023)
2-201807605-T-G		not specified	Uncertain significance (Nov 17, 2022)
2-201807870-C-G		not specified	Uncertain significance (Nov 18, 2022)
2-201807897-A-T		not specified	Uncertain significance (Nov 23, 2024)
2-201807919-G-C		not specified	Uncertain significance (Jul 27, 2021)
2-201807928-C-T		not specified	Uncertain significance (Dec 10, 2024)
2-201812538-G-A		not specified	Uncertain significance (Dec 21, 2022)
2-201812538-G-C		not specified	Uncertain significance (Sep 03, 2024)
2-201812557-G-A		not specified	Uncertain significance (Dec 26, 2023)
2-201822811-T-A		not specified	Uncertain significance (Nov 09, 2021)
2-201822830-A-G		not specified	Uncertain significance (Sep 22, 2022)
2-201822872-A-G		not specified	Uncertain significance (Sep 09, 2024)
2-201822889-G-A		not specified	Uncertain significance (Oct 04, 2024)
2-201833882-A-G		not specified	Uncertain significance (Jul 22, 2024)
2-201835730-G-A		not specified	Uncertain significance (Aug 26, 2024)
2-201835736-C-T		not specified	Uncertain significance (Feb 21, 2024)
2-201835750-G-A		not specified	Uncertain significance (Feb 06, 2024)
2-201847428-T-C		not specified	Uncertain significance (Jun 20, 2024)
2-201847446-T-A		not specified	Uncertain significance (Jan 03, 2024)
2-201854893-A-G		not specified	Uncertain significance (Dec 15, 2022)
2-201854928-T-C		not specified	Uncertain significance (Apr 12, 2023)
2-201872293-C-T		not specified	Uncertain significance (May 16, 2024)
2-201872324-C-A		not specified	Uncertain significance (Apr 23, 2024)
2-201880032-G-C		not specified	Uncertain significance (Nov 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDK15	protein_coding	protein_coding	ENST00000450471	13	105090

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.24e-17	0.00771	125277	2	469	125748	0.00187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00459	239	239	1.00	0.0000126	2794
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00682	0.00676
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00103	0.00103
Finnish	0.00245	0.00245
European (Non-Finnish)	0.00171	0.00170
Middle Eastern	0.00103	0.00103
South Asian	0.00190	0.00190
Other	0.000653	0.000652

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.162
• hipred: N
• hipred_score: 0.289
• ghis: 0.429

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: Cdk15

Gene ontology

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