CDK19

cyclin dependent kinase 19, the group of Cyclin dependent kinases|Mediator complex

Basic information

Region (hg38): 6:110609977-110815958

Previous symbols: [ "CDK11", "CDC2L6" ]

Links

ENSG00000155111 ∙ NCBI:23097 ∙ OMIM:614720 ∙ HGNC:19338 ∙ Uniprot:Q9BWU1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• developmental and epileptic encephalopathy, 87 (Limited), mode of inheritance: AD
• undetermined early-onset epileptic encephalopathy (Supportive), mode of inheritance: AD
• developmental and epileptic encephalopathy, 87 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Developmental and epileptic encephalopathy 87	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Neurologic	32330417

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDK19 gene.

• not provided (15 variants)
• Inborn genetic diseases (11 variants)
• Developmental and epileptic encephalopathy, 87 (9 variants)
• not specified (2 variants)
• See cases (2 variants)
• CDK19-related condition (1 variants)
• Neurodevelopmental disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDK19 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		4
missense	3	3	17	2		25
nonsense						0
start loss						0
frameshift			2			2
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			1	1		2
non coding			2	1		3
Total	3	3	22	7	0

Variants in CDK19

This is a list of pathogenic ClinVar variants found in the CDK19 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-110614542-C-T		Inborn genetic diseases	Uncertain significance (Oct 02, 2023)
6-110614558-A-T		Developmental and epileptic encephalopathy, 87	Uncertain significance (-)
6-110614561-G-T			Uncertain significance (Mar 03, 2023)
6-110614618-G-C		Inborn genetic diseases	Uncertain significance (Mar 02, 2023)
6-110614633-C-T		Inborn genetic diseases	Uncertain significance (Jul 14, 2021)
6-110621175-G-T		Inborn genetic diseases	Uncertain significance (Jun 23, 2023)
6-110621224-G-A			Likely benign (Oct 01, 2022)
6-110621232-C-T		Inborn genetic diseases	Uncertain significance (Oct 26, 2022)
6-110621234-A-G		Inborn genetic diseases	Likely benign (May 31, 2023)
6-110621263-G-C		Inborn genetic diseases	Uncertain significance (May 22, 2023)
6-110621291-G-T		Inborn genetic diseases	Uncertain significance (Jun 22, 2023)
6-110621297-G-A		Microcephaly	Uncertain significance (-)
6-110621298-CCTGTGGAGGGGCTGCTGCCTG-C			Uncertain significance (Dec 31, 2022)
6-110621340-G-C			Uncertain significance (Jun 09, 2022)
6-110621365-C-A		Inborn genetic diseases	Uncertain significance (Oct 17, 2023)
6-110622157-G-A			Likely benign (Oct 01, 2023)
6-110622894-T-C		See cases	Uncertain significance (Dec 28, 2021)
6-110622905-T-C		Inborn genetic diseases	Uncertain significance (Aug 08, 2023)
6-110623334-T-C			Uncertain significance (Nov 18, 2021)
6-110627028-A-G		Neurodevelopmental disorder	Uncertain significance (Nov 25, 2020)
6-110627069-TA-T			Uncertain significance (Jul 18, 2022)
6-110632078-G-A			Likely pathogenic (Jul 12, 2020)
6-110632082-C-G		Developmental and epileptic encephalopathy, 87	Uncertain significance (Dec 16, 2021)
6-110632087-A-G		Developmental and epileptic encephalopathy, 87	Likely pathogenic (Aug 11, 2020)
6-110632090-T-C		Developmental and epileptic encephalopathy, 87 • CDK19-related disorder • Inborn genetic diseases	Conflicting classifications of pathogenicity (Oct 08, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDK19	protein_coding	protein_coding	ENST00000368911	13	205981

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000179	125660	0	3	125663	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.56	114	283	0.403	0.0000145	3311
Missense in Polyphen		20	100.68	0.19864		1213
Synonymous	0.871	93	104	0.891	0.00000572	925
Loss of Function	4.82	1	29.0	0.0345	0.00000143	337

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000358	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Developmental Biology;Transcriptional regulation of white adipocyte differentiation (Consensus)

Recessive Scores

• pRec: 0.0850

Intolerance Scores

• loftool: 0.0675
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.580
• hipred: Y
• hipred_score: 0.786
• ghis: 0.572

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: Cdk19

Gene ontology

• Biological process: protein phosphorylation;positive regulation of apoptotic process;positive regulation of inflammatory response;regulation of cell cycle;cellular response to lipopolysaccharide
• Cellular component: nucleus;cytosol;mediator complex
• Molecular function: cyclin-dependent protein serine/threonine kinase activity;ATP binding;enzyme binding