CSNK2B

protein-coding

casein 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

NM_001320.7

Inheritance

AD

ClinVar variants

P:127U:70B:14

Top phenotype

Poirier-Bienvenu neurodevelopmental syndrome

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr6:31,665,227-31,670,343

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~5.1 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Poirier-Bienvenu neurodevelopmental syndromeDEFINITIVE

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).

Poirier-Bienvenu neurodevelopmental syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0032889

Submitter: Labcorp Genetics (formerly Invitae)

Poirier-Bienvenu neurodevelopmental syndromeDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0032889

Submitter: Illumina

Poirier-Bienvenu neurodevelopmental syndromeDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0032889

Submitter: G2P

Poirier-Bienvenu neurodevelopmental syndromeDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0032889

Submitter: Ambry Genetics

autosomal dominant non-syndromic intellectual disabilitySUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0015802

Submitter: Orphanet

Clinical Genomic Database (CGD)

Poirier-Bienvenu neurodevelopmental syndromeAD

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

Refs: 28585349; 28762608; 30655572; 31784560Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CSNK2B variants in ClinVar

27 Conditions Cataloged
not providedTotal: 111
Poirier-Bienvenu neurodevelopmental syndromeTotal: 103
CSNK2B-related disorderTotal: 34
Inborn genetic diseasesTotal: 28
not specifiedTotal: 13
Intellectual disabilityTotal: 3
SeizureTotal: 2
Neurodevelopmental disorderTotal: 2

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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
14
clinvar
17
missense
8
clinvar
24
clinvar
60
clinvar
92
nonsense
18
clinvar
10
clinvar
1
clinvar
29
start loss
1
clinvar
4
clinvar
5
frameshift
20
clinvar
15
clinvar
3
clinvar
38
splice donor/acceptor (+/-2bp)
13
clinvar
14
clinvar
3
clinvar
30
Total606770140211

Highest pathogenic variant AF is 0.000021917327

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001320.7RefSeqNP_001311.36MANE Select
ENST00000375882.7EnsemblENSP00000365042.36MANE Select
NM_001282385.2RefSeqNP_001269314.16Standard
ENST00000375865.6EnsemblENSP00000365025.26Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense3.13271260.2150.000006951430
Missense (PolyPhen)648.7220.12315529
Synonymous0.9143947.00.8300.00000291371
Loss of Function3.00112.40.08075.83e-7144

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.00000880.0000088rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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