CSNK2B
protein-codingcasein kinase 2 beta
Gene summary
This gene encodes the beta subunit of casein kinase II, a ubiquitous protein kinase which regulates metabolic pathways, signal transduction, transcription, translation, and replication. The enzyme is composed of three subunits, alpha, alpha prime and beta, which form a tetrameric holoenzyme. The alpha and alpha prime subunits are catalytic, while the beta subunit serves regulatory functions. The enzyme localizes to the endoplasmic reticulum and the Golgi apparatus. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~5.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0032889
Submitter: ClinGen
The CSNK2B gene is located on chromosome 6 at 6p21.33 and encodes the casein kinase 2 beta protein, the regulatory subunit of casein kinase 2 (CK2). The CK-beta subunits form homodimers at the core of the CK2 enzyme and are thought to contribute to the stability of the holoenzyme complex, regulating the catalytic activity and substrate recognition. CK2 is a ubiquitously expressed serine threonine kinase and plays a role in many cellular processes. CSNK2B was first reported in relation to autosomal dominant Poirier-Bienvenu neurodevelopmental syndrome in 2017 (Poirier et al., PMID: 28585349). This disorder is characterized by mild to profound intellectual disability, with or without epilepsy. The epilepsy is often early-onset occurring before three years of age, often intractable with the most common seizure type being generalized tonic-clonic seizures (Nakashima et al., 2019, PMID: 30655572; Li et al., 2019, PMID: 31784560; Ernst et al., 2021, PMID: 34041744). The presentation is variable. Other phenotypes commonly seen in patients include global developmental delays with mild to severe delayed psychomotor development, speech and language delay, facial dysmorphic features and growth abnormalities (PMID: 28585349; Sakaguchi et al., 2017, PMID: 28762608; PMIDs: 30655572, 31784560; Selvam et al., 2021, PMID: 33166063). Some affected individuals also exhibit autistic features, hypotonia, dystonia, and cerebral atrophy (PMID: 34041744). Evidence supporting this gene-disease relationship includes case-level data and experimental data. Variants in this gene have been reported in at least ten unrelated individuals in five publications. At least ten unique variants have been reported and include a spectrum of missense, splice site, frameshift, and nonsense variants. Variants typically occur de novo. More evidence is available in the literature, but the maximum score for genetic evidence (12 pts.) has been reached. This gene-disease relationship is also supported by a temporal and spatial expression pattern of CK2 which is consistent with disease and studies reducing expression levels of Csnk2b mouse in neural stem cells and primary hippocampal neurons support a role for CSNK2B in the regulation of neuronal proliferation and differentiation as well as the modulation of synaptic transmission (Blanquet 2000, PMID: 10658642; Yang et al., 2018, PMID: 29483533). Furthermore, the CSNK2A gene which also encodes a subunit of CK2 holoenzyme, is associated with Okur-Chung neurodevelopmental syndrome and a similar phenotypic spectrum of disease (Okur et al., 2016; PMID: 27048600). In summary, CSNK2B is definitively associated with autosomal dominant Poirier-Bienvenu neurodevelopmental syndrome. This has been repeatedly demonstrated in both the research and clinical diagnostic settings and has been upheld over time. This classification was approved by the ClinGen Syndromic Disorders Gene Curation Expert Panel on the meeting date 01.21.2022 (SOP Version 8).
Inheritance Pattern: AD
Disease ID:MONDO:0032889
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0032889
Submitter: Illumina
Inheritance Pattern: AD
Disease ID:MONDO:0032889
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0032889
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0015802
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Dental; Neurologic
Intervention: General
Rationale: 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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CSNK2B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001320.7. 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 | 3 | 14 | 17 | |||
| missense | 8 | 24 | 60 | 92 | ||
| nonsense | 18 | 10 | 1 | 29 | ||
| start loss | 1 | 4 | 5 | |||
| frameshift | 20 | 15 | 3 | 38 | ||
| splice donor/acceptor (+/-2bp) | 13 | 14 | 3 | 30 | ||
| Total | 60 | 67 | 70 | 14 | 0 | 211 |
Highest pathogenic variant AF is 0.000021917327
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001311.3 | 6 | MANE Select | |
| Ensembl | ENSP00000365042.3 | 6 | MANE Select | |
| RefSeq | NP_001269314.1 | 6 | Standard | |
| Ensembl | ENSP00000365025.2 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Adherens junction - Homo sapiens (human)
- Ribosome biogenesis in eukaryotes - Homo sapiens (human)
- Mitophagy - animal - Homo sapiens (human)
- Measles - Homo sapiens (human)
- Wnt signaling pathway - Homo sapiens (human)
Biological Process
- signal transduction
- negative regulation of cell population proliferation
- positive regulation of pathway-restricted SMAD protein phosphorylation
- Wnt signaling pathway
- peptidyl-threonine phosphorylation
Molecular Function
- chromatin binding
- protein serine/threonine kinase activity
- signaling receptor binding
- protein binding
- transcription factor binding
Cellular Component
- chromatin
- extracellular region
- nucleus
- nucleoplasm
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000375882
- Coding exons
- 6
- Length
- 5108
- Individuals with no LoFs
- 125701
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 125703
- p
- 0.00000796
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.13 | 27 | 126 | 0.215 | 0.00000695 | 1430 |
| Missense (PolyPhen) | 6 | 48.722 | 0.12315 | 529 | ||
| Synonymous | 0.914 | 39 | 47.0 | 0.830 | 0.00000291 | 371 |
| Loss of Function | 3.00 | 1 | 12.4 | 0.0807 | 5.83e-7 | 144 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0000088 | 0.0000088 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Participates in Wnt signaling (By similarity). Plays a complex role in regulating the basal catalytic activity of the alpha subunit. {ECO:0000250, ECO:0000269|PubMed:11239457, ECO:0000269|PubMed:16818610}.;
Recessive Scores
- pRec
- 0.201
Intolerance Scores
- LoFtool
- 0.116
- RVIS EVS
- -0.1
- RVIS percentile EVS
- 46.2
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |