CDK11B

cyclin dependent kinase 11B, the group of Cyclin dependent kinases

Basic information

Region (hg38): 1:1635225-1659012

Previous symbols: [ "CDC2L1" ]

Links

ENSG00000248333 ∙ NCBI:984 ∙ OMIM:176873 ∙ HGNC:1729 ∙ Uniprot:P21127 ∙ 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 CDK11B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDK11B 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				5		5
missense			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	5	0

Variants in CDK11B

This is a list of pathogenic ClinVar variants found in the CDK11B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-1636951-G-C		not specified	Likely benign (Dec 19, 2023)
1-1637120-C-T		not specified	Likely benign (Aug 04, 2023)
1-1637774-G-A			Likely benign (Jan 01, 2023)
1-1640331-G-A		not specified	Likely benign (Aug 02, 2023)
1-1640370-G-A			Likely benign (Oct 01, 2023)
1-1640376-C-T		not specified	Likely benign (Jun 03, 2024)
1-1652469-G-C		not specified	Uncertain significance (Dec 13, 2021)
1-1655477-T-C		Seizure	Uncertain significance (Jan 01, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDK11B	protein_coding	protein_coding	ENST00000407249	21	19871

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000648	0.999	124673	0	23	124696	0.0000922

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.72	223	308	0.724	0.0000192	5054
Missense in Polyphen		24	37.484	0.64027		708
Synonymous	-3.78	186	131	1.42	0.00000900	1369
Loss of Function	2.89	12	28.7	0.418	0.00000139	541

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000459	0.000445
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000511	0.0000464
European (Non-Finnish)	0.000111	0.000106
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.000170	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays multiple roles in cell cycle progression, cytokinesis and apoptosis. Involved in pre-mRNA splicing in a kinase activity-dependent manner. Isoform 7 may act as a negative regulator of normal cell cycle progression. {ECO:0000269|PubMed:12501247, ECO:0000269|PubMed:12624090, ECO:0000269|PubMed:18216018, ECO:0000269|PubMed:2217177}.
• Pathway: hiv-1 nef: negative effector of fas and tnf;AndrogenReceptor;terminal <i>O</i>-glycans residues modification;Recruitment of mitotic centrosome proteins and complexes;Centrosome maturation;Coregulation of Androgen receptor activity;G2/M Transition;Mitotic G2-G2/M phases;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.141

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.459
• ghis: 0.498

Essentials

• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdk11b
• Phenotype: embryo phenotype; neoplasm; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cellular phenotype

Gene ontology

• Biological process: mitotic cell cycle;regulation of cell growth;regulation of transcription, DNA-templated;protein phosphorylation;apoptotic process;cell population proliferation;regulation of mRNA processing;regulation of cell cycle
• Cellular component: nucleus;cytoplasm
• Molecular function: RNA binding;protein kinase activity;protein serine/threonine kinase activity;cyclin-dependent protein serine/threonine kinase activity;protein binding;ATP binding