CDK13

cyclin dependent kinase 13, the group of Cyclin dependent kinases

Basic information

Region (hg38): 7:39950121-40099580

Previous symbols: [ "CDC2L5" ]

Links

ENSG00000065883

∙ NCBI:8621 ∙ OMIM:603309 ∙ HGNC:1733 ∙ Uniprot:Q14004 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

congenital heart defects, dysmorphic facial features, and intellectual developmental disorder (Strong), mode of inheritance: AD
congenital heart defects, dysmorphic facial features, and intellectual developmental disorder (Strong), mode of inheritance: AD
syndromic intellectual disability (Definitive), mode of inheritance: AD
congenital heart defects, dysmorphic facial features, and intellectual developmental disorder (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder	AD	Cardiovascular	The condition can involve congenital cardiac anomalies, and awareness may allow early management	Cardiovascular; Craniofacial; Musculoskeletal; Neurologic	27479907

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDK13 gene.

not_provided (814 variants)
Inborn_genetic_diseases (203 variants)
Congenital_heart_defects,_dysmorphic_facial_features,_and_intellectual_developmental_disorder (118 variants)
CDK13-related_disorder (53 variants)
not_specified (23 variants)
Intellectual_disability (5 variants)
Global_developmental_delay (3 variants)
See_cases (3 variants)
Syndromic_intellectual_disability (2 variants)
Wolfram-like_disorder (1 variants)
Neurodevelopmental_disorder (1 variants)
Autism_spectrum_disorder (1 variants)
Neurodevelopmental_delay (1 variants)
Marfanoid_habitus_and_intellectual_disability (1 variants)
Neurodevelopmental_abnormality (1 variants)
Heart,_malformation_of (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDK13 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003718.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	214 clinvar	14 clinvar	230
missense	13 clinvar	33 clinvar	433 clinvar	105 clinvar	34 clinvar	618
nonsense	12 clinvar	13 clinvar	14 clinvar			39
start loss						0
frameshift	10 clinvar	12 clinvar	20 clinvar			42
splice donor/acceptor (+/-2bp)		1 clinvar	4 clinvar			5
Total	35	59	473	319	48

Highest pathogenic variant AF is 0.000040263614

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDK13	protein_coding	protein_coding	ENST00000181839	14	147098

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.908	0.0925	125733	0	14	125747	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.35	510	683	0.747	0.0000357	9669
Missense in Polyphen		158	309.35	0.51075		3862
Synonymous	-1.51	292	261	1.12	0.0000137	3100
Loss of Function	5.58	11	56.2	0.196	0.00000328	720

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000628	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000659	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Cyclin-dependent kinase which displays CTD kinase activity and is required for RNA splicing. Has CTD kinase activity by hyperphosphorylating the C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit RPB1, thereby acting as a key regulator of transcription elongation. Required for RNA splicing, probably by phosphorylating SRSF1/SF2. Required during hematopoiesis. In case of infection by HIV-1 virus, interacts with HIV-1 Tat protein acetylated at 'Lys-50' and 'Lys- 51', thereby increasing HIV-1 mRNA splicing and promoting the production of the doubly spliced HIV-1 protein Nef. {ECO:0000269|PubMed:16721827, ECO:0000269|PubMed:1731328, ECO:0000269|PubMed:18480452, ECO:0000269|PubMed:20952539}.;
Disease: DISEASE: Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder (CHDFIDD) [MIM:617360]: An autosomal dominant syndrome characterized by atrial and/or ventricular septal congenital heart defects, facial dysmorphism with hypertelorism, upslanted palpebral fissures, epicanthal folds, ptosis, strabismus, posteriorly rotated ears, thin upper lip, and small mouth. Patients manifest global developmental delay, delayed walking and speech acquisition, and intellectual disability. Some patients have mild microcephaly, a small cerebral cortex, and agenesis of corpus callosum. More variable features include clinodactyly and/or camptodactyly of the fingers, hypotonia, and joint hypermobility. {ECO:0000269|PubMed:27479907, ECO:0000269|PubMed:28807008}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Neutrophil degranulation;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Innate Immune System;Immune System;TP53 Regulates Transcription of DNA Repair Genes;Transcriptional Regulation by TP53 (Consensus)

Recessive Scores

pRec: 0.226

Intolerance Scores

loftool: 0.569
rvis_EVS: -1.08
rvis_percentile_EVS: 7.28

Haploinsufficiency Scores

pHI: 0.258
hipred: Y
hipred_score: 0.682
ghis: 0.675

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: S
essential_gene_gene_trap: K
gene_indispensability_pred: E
gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cdk13
Phenotype

Gene ontology

Biological process: alternative mRNA splicing, via spliceosome;transcription elongation from RNA polymerase II promoter;protein phosphorylation;regulation of mitotic nuclear division;multicellular organism development;positive regulation of cell population proliferation;viral process;hemopoiesis;positive regulation of transcription elongation from RNA polymerase II promoter;neutrophil degranulation;positive regulation of transcription by RNA polymerase II;phosphorylation of RNA polymerase II C-terminal domain;negative regulation of stem cell differentiation
Cellular component: cyclin-dependent protein kinase holoenzyme complex;nuclear chromatin;cyclin K-CDK13 complex;extracellular region;extracellular space;nucleus;nucleoplasm;chromosome;Golgi apparatus;cytosol;cyclin/CDK positive transcription elongation factor complex;nuclear speck;nuclear cyclin-dependent protein kinase holoenzyme complex;ficolin-1-rich granule lumen
Molecular function: RNA binding;protein kinase activity;cyclin-dependent protein serine/threonine kinase activity;protein binding;ATP binding;transcription factor binding;RNA polymerase II CTD heptapeptide repeat kinase activity;protein kinase binding;cyclin binding;transcription regulatory region DNA binding