CDK16

cyclin dependent kinase 16, the group of Cyclin dependent kinases

Basic information

Region (hg38): X:47217860-47229997

Previous symbols: [ "PCTK1" ]

Links

ENSG00000102225 ∙ NCBI:5127 ∙ OMIM:311550 ∙ HGNC:8749 ∙ Uniprot:Q00536 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability, autosomal dominant 40 (Limited), mode of inheritance: XLR
• intellectual disability, autosomal dominant 40 (Limited), mode of inheritance: XL
• X-linked complex neurodevelopmental disorder (Limited), mode of inheritance: XL

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDK16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDK16 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				4	1	5
missense			20		1	21
nonsense			2			2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			3		2	5
non coding			4		4	8
Total	0	0	27	4	6

Variants in CDK16

This is a list of pathogenic ClinVar variants found in the CDK16 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-47218661-C-G			Likely benign (Apr 01, 2022)
X-47218663-AG-A		CDK16-related disorder	Uncertain significance (Apr 21, 2023)
X-47223121-A-G		CDK16-related disorder	Benign (Jun 11, 2019)
X-47223136-C-T		Intellectual disability	Uncertain significance (Feb 04, 2020)
X-47223151-C-T		not specified	Uncertain significance (Sep 16, 2021)
X-47223217-C-G		not specified • CDK16-related disorder	Benign (May 14, 2015)
X-47223234-G-A		not specified	Uncertain significance (Jan 23, 2023)
X-47223273-C-T		not specified	Benign (Dec 01, 2014)
X-47223288-A-G		not specified	Uncertain significance (Jan 24, 2024)
X-47223553-T-G		not specified	Uncertain significance (Dec 21, 2022)
X-47223642-G-A		not specified	Uncertain significance (May 04, 2022)
X-47223706-G-A		not specified	Uncertain significance (Mar 02, 2023)
X-47223750-T-C		CDK16-related disorder	Uncertain significance (Sep 12, 2024)
X-47224391-T-C			Uncertain significance (Oct 01, 2020)
X-47224399-G-A		not specified	Uncertain significance (Apr 16, 2024)
X-47224480-C-T		not specified	Uncertain significance (Jul 19, 2023)
X-47224489-A-G		not specified	Uncertain significance (Aug 21, 2023)
X-47224501-C-G		not specified	Uncertain significance (Dec 09, 2023)
X-47224633-C-T		CDK16-related disorder	Likely benign (Sep 19, 2019)
X-47224638-A-G		CDK16-related disorder	Benign (Jun 11, 2019)
X-47224642-C-T			Uncertain significance (Mar 01, 2022)
X-47224742-T-A		not specified	Uncertain significance (Apr 20, 2023)
X-47224750-A-T			Benign (Sep 17, 2018)
X-47225031-A-C		not specified	Uncertain significance (Apr 07, 2022)
X-47225864-C-T			Uncertain significance (May 20, 2013)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDK16	protein_coding	protein_coding	ENST00000276052	16	12138

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.995	0.00520	123854	0	1	123855	0.00000404

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.91	122	252	0.484	0.0000222	3673
Missense in Polyphen		27	106.58	0.25334		1595
Synonymous	1.32	84	101	0.833	0.00000864	1183
Loss of Function	4.20	2	24.4	0.0819	0.00000217	346

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000722	0.0000545
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000722	0.0000545
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein kinase that plays a role in vesicle-mediated transport processes and exocytosis. Regulates GH1 release by brain neurons. Phosphorylates NSF, and thereby regulates NSF oligomerization. Required for normal spermatogenesis. Regulates neuron differentiation and dendrite development (By similarity). Plays a role in the regulation of insulin secretion in response to changes in blood glucose levels. Can phosphorylate CCNY at 'Ser- 336' (in vitro). {ECO:0000250, ECO:0000269|PubMed:22184064, ECO:0000269|PubMed:22796189, ECO:0000269|PubMed:22798068}.

Recessive Scores

• pRec: 0.150

Intolerance Scores

• loftool: 0.370
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.330
• hipred: Y
• hipred_score: 0.701
• ghis: 0.538

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: Cdk16
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype

Gene ontology

• Biological process: protein phosphorylation;exocytosis;spermatogenesis;growth hormone secretion;neuron projection development;regulation of cell cycle;regulation of insulin secretion involved in cellular response to glucose stimulus
• Cellular component: nucleus;cytoplasm;cytosol;plasma membrane;synaptic vesicle;microtubule cytoskeleton;cell junction;extrinsic component of cytoplasmic side of plasma membrane;neuron projection
• Molecular function: protein serine/threonine kinase activity;cyclin-dependent protein serine/threonine kinase activity;protein binding;ATP binding