CDK11B

protein-coding

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

Gene summary

This gene encodes a member of the serine/threonine protein kinase family. Members of this kinase family are known to be essential for eukaryotic cell cycle control. Due to a segmental duplication, this gene shares very high sequence identity with a neighboring gene. These two genes are frequently deleted or altered in neuroblastoma. The protein kinase encoded by this gene can be cleaved by caspases and may play a role in cell apoptosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2014]

Previous symbols:

CDC2L1

MANE transcript

NM_033486.3

Inheritance

—

ClinVar variants

U:9B:9

Top phenotype

Brachymorphism-onychodysplasia-dysphalangism syndrome

gnomAD constraint

pLI —, LoF o/e 0.42

Max pathogenic AF

—

Genomic locus

chr1:1,635,225-1,659,012

External References & Databases

Ensembl (ENSG00000248333)

Transcript & Mutation Effects

hg38 • Region Span ~23.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CDK11B variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 7

not providedTotal: 4

Brachymorphism-onychodysplasia-dysphalangism syndromeTotal: 2

SeizureTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033486.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	9 clinvar		11
missense			4 clinvar			4
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	9	9	0	18

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 68 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033486.3	RefSeq	NP_277021.2	19	MANE Select
ENST00000341832.11	Ensembl	ENSP00000463048.2	19	MANE Select
NM_001291345.2	RefSeq	NP_001278274.1	19	Standard
NM_001787.3	RefSeq	NP_001778.2	19	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

mitotic cell cycle
regulation of cell growth
regulation of transcription, DNA-templated
protein phosphorylation
apoptotic process

Molecular Function

RNA binding
protein kinase activity
protein serine/threonine kinase activity
cyclin-dependent protein serine/threonine kinase activity
protein binding

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000407249
Coding exons: 21
Length: 19871
Individuals with no LoFs: 124673
Homozygous LoFs: 0
Heterozygous LoFs: 23
Defined: 124696
p: 0.0000922

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.72	223	308	0.724	0.0000192	5054
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00040	0.00039	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000051	0.000046	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.000033	0.000033	rare
Other	0.00017	0.00017	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.141

Essentials

Indispensability pred.: E
Indispensability score: 0.781

Gene Damage Prediction

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