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Relevance to Autism

Two rare de novo missense variants in the CSNK2A1 gene have been identified in ASD probands from simplex families from the Simons Simplex Collection (Iossifov et al., 2014) and the ASD: Genomes to Outcome Study cohort (Yuen et al., 2017). Heterozygous variants in the CSNK2A1 gene are also responsible for Okur-Chung neurodevelopmental syndrome (OMIM 617062), an autosomal dominant disorder characterized by delayed psychomotor development, intellectual disability with poor speech, behavioral abnormalities, cortical malformations in some patients, and variable dysmorphic facial features; autistic features and/or stereotypy has been reported in a subset of affected individuals (Okur et al., 2016; Trinh et al., 2017; Chiu et al., 2018; Owen et al., 2018, Martinez-Monseny et al., 2020).

Molecular Function

Casein kinase II is a serine/threonine protein kinase that phosphorylates acidic proteins such as casein. It is involved in various cellular processes, including cell cycle control, apoptosis, and circadian rhythm. The kinase exists as a tetramer and is composed of an alpha, an alpha-prime, and two beta subunits. The alpha subunits contain the catalytic activity while the beta subunits undergo autophosphorylation. The protein encoded by this gene represents the alpha subunit.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
The contribution of de novo coding mutations to autism spectrum disorder
ASD
Support
Okur-Chung neurodevelopmental syndrome in a patient from Spain
Okur-Chung neurodevelopmental syndrome, DD, ID
Stereotypy
Support
De novo mutations in CSNK2A1 are associated with neurodevelopmental abnormalities and dysmorphic features
Okur-Chung neurodevelopmental syndrome, DD, ID
ADHD, epilepsy/seizures, stereotypy
Support
Identification of de novo CSNK2A1 and CSNK2B variants in cases of global developmental delay with seizures
DD, epilepsy/seizures
ID
Support
The Okur-Chung Neurodevelopmental Syndrome Mutation CK2 K198R Leads to a Rewiring of Kinase Specificity
Okur-Chung neurodevelopmental syndrome
Support
Diagnostic yield of clinical exome sequencing in 868 children with neurodevelopmental disorders
ASD, DD
Support
Refining the clinical phenotype of Okur-Chung neurodevelopmental syndrome
Okur-Chung neurodevelopmental syndrome, DD, ID
Support
Mutational Landscape of Autism Spectrum Disorder Brain Tissue
ASD
Support
Expanding the phenotypic spectrum of CSNK2A1-associated Okur-Chung neurodevelopmental syndrome
Okur-Chung neurodevelopmental syndrome, DD, ID
ASD, epilepsy/seizures
Support
Extending the phenotype associated with the CSNK2A1-related Okur-Chung syndrome-A clinical study of 11 individuals
Okur-Chung neurodevelopmental syndrome, ID
Autistic features, stereotypy
Support
Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders
ASD, DD
Support
Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings
DD
Support
Okur-Chung neurodevelopmental syndrome: Eight additional cases with implications on phenotype and genotype expansion
Okur-Chung neurodevelopmental syndrome, DD, ID
ASD or autistic features, stereotypy, epilepsy/sei
Support
Dual molecular diagnosis of tricho-rhino-phalangeal syndrome type I and Okur-Chung neurodevelopmental syndrome in one Chinese patient: a case report
Okur-Chung neurodevelopmental syndrome, DD, ID
Impaired social interactions
Support
Phenotypic and genetic analysis of children with unexplained neurodevelopmental delay and neurodevelopmental comorbidities in a Chinese cohort using trio-based whole-exome sequencing
DD, ID
ASD, ADHD, epilepsy/seizures
Support
A novel de novo mutation in CSNK2A1: reinforcing the link to neurodevelopmental abnormalities and dysmorphic features
Okur-Chung neurodevelopmental syndrome, DD, ID
Autistic features
Support
Overrepresentation of genetic variation in the AnkyrinG interactome is related to a range of neurodevelopmental disorders
DD
ASD, epilepsy/seizures
Support
The utility of exome sequencing in diagnosing pediatric neurodevelopmental disorders in a highly consanguineous population
DD
Support
Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder
ASD
Recent Recommendation
Missense mutation in the activation segment of the kinase CK2 models Okur-Chung neurodevelopmental disorder and alters the hippocampal glutamatergic synapse
Okur-Chung neurodevelopmental syndrome
Recent Recommendation
Okur-Chung neurodevelopmental syndrome-linked CK2α variants have reduced kinase activity
Okur-Chung neurodevelopmental syndrome
ASD

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN1196R001 
 missense_variant 
 c.593A>G 
 p.Lys198Arg 
 De novo 
  
 Simplex 
 GEN1196R002 
 missense_variant 
 c.79G>A 
 p.Glu27Lys 
 De novo 
  
 Simplex 
 GEN1196R003 
 missense_variant 
 c.593A>G 
 p.Lys198Arg 
 De novo 
  
 Simplex 
 GEN1196R004 
 missense_variant 
 c.479A>G 
 p.His160Arg 
 De novo 
  
 Simplex 
 GEN1196R005 
 missense_variant 
 c.140G>A 
 p.Arg47Gln 
 De novo 
  
  
 GEN1196R006 
 missense_variant 
 c.593A>G 
 p.Lys198Arg 
 De novo 
  
  
 GEN1196R007 
 missense_variant 
 c.524A>G 
 p.Asp175Gly 
 De novo 
  
  
 GEN1196R008 
 splice_site_variant 
 c.824+2T>C 
  
 De novo 
  
  
 GEN1196R009 
 missense_variant 
 c.149A>C 
 p.Tyr50Ser 
 De novo 
  
  
 GEN1196R010 
 missense_variant 
 c.466G>C 
 p.Asp156His 
 De novo 
  
 Simplex 
 GEN1196R011 
 missense_variant 
 c.593A>G 
 p.Lys198Arg 
 De novo 
  
  
 GEN1196R012 
 missense_variant 
 c.692C>G 
 p.Pro231Arg 
 De novo 
  
  
 GEN1196R013 
 missense_variant 
 c.79G>A 
 p.Glu27Lys 
 De novo 
  
  
 GEN1196R014 
 missense_variant 
 c.1A>G 
 p.Met1? 
 De novo 
  
  
 GEN1196R015 
 missense_variant 
 c.218T>A 
 p.Val73Glu 
 De novo 
  
  
 GEN1196R016 
 missense_variant 
 c.140G>A 
 p.Arg47Gln 
 De novo 
  
  
 GEN1196R017 
 missense_variant 
 c.935G>A 
 p.Arg312Gln 
 De novo 
  
  
 GEN1196R018 
 missense_variant 
 c.151A>C 
 p.Ser51Arg 
 De novo 
  
  
 GEN1196R019 
 missense_variant 
 c.140G>A 
 p.Arg47Gln 
 De novo 
  
  
 GEN1196R020 
 missense_variant 
 c.152G>A 
 p.Ser51Asn 
 De novo 
  
  
 GEN1196R021 
 missense_variant 
 c.239G>A 
 p.Arg80His 
 De novo 
  
  
 GEN1196R022 
 missense_variant 
 c.522A>G 
 p.Ile174Met 
 De novo 
  
  
 GEN1196R023 
 missense_variant 
 c.572G>A 
 p.Arg191Gln 
 De novo 
  
  
 GEN1196R024 
 missense_variant 
 c.589T>A 
 p.Phe197Ile 
 De novo 
  
  
 GEN1196R025 
 missense_variant 
 c.593A>G 
 p.Lys198Arg 
 De novo 
  
  
 GEN1196R026 
 missense_variant 
 c.593A>G 
 p.Lys198Arg 
 De novo 
  
  
 GEN1196R027 
 missense_variant 
 c.593A>G 
 p.Lys198Arg 
 De novo 
  
  
 GEN1196R028 
 missense_variant 
 c.593A>G 
 p.Lys198Arg 
 De novo 
  
  
 GEN1196R029 
 missense_variant 
 c.934C>T 
 p.Arg312Trp 
 De novo 
  
  
 GEN1196R030 
 missense_variant 
 c.593A>G 
 p.Lys198Arg 
 De novo 
  
 Simplex 
 GEN1196R031 
 missense_variant 
 c.593A>G 
 p.Lys198Arg 
 De novo 
  
  
 GEN1196R032 
 stop_gained 
 c.571C>T 
 p.Arg191Ter 
 De novo 
  
  
 GEN1196R033 
 missense_variant 
 c.149A>G 
 p.Tyr50Cys 
 De novo 
  
  
 GEN1196R034 
 missense_variant 
 c.593A>G 
 p.Lys198Arg 
 Familial 
 Paternal 
 Simplex 
 GEN1196R035 
 splice_site_variant 
 c.973+1G>C 
  
 De novo 
  
  
 GEN1196R036 
 missense_variant 
 c.116A>G 
 p.Tyr39Cys 
 De novo 
  
  
 GEN1196R037 
 stop_gained 
 c.916C>T 
 p.Arg306Ter 
 De novo 
  
  
 GEN1196R038 
 missense_variant 
 c.440G>A 
 p.Cys147Tyr 
 Unknown 
  
  
 GEN1196R039 
 splice_site_variant 
 c.973+1G>A 
  
 Unknown 
  
  
 GEN1196R040 
 stop_gained 
 c.319C>T 
 p.Arg107Ter 
 Unknown 
  
  
 GEN1196R041 
 stop_gained 
 c.571C>T 
 p.Arg191Ter 
 Unknown 
  
  
 GEN1196R042 
 stop_gained 
 c.583C>T 
 p.Arg195Ter 
 Unknown 
 Not maternal 
  
 GEN1196R043 
 missense_variant 
 c.152G>T 
 p.Ser51Ile 
 Unknown 
  
  
 GEN1196R044 
 missense_variant 
 c.298A>G 
 p.Ile100Val 
 Unknown 
  
  
 GEN1196R045 
 missense_variant 
 c.593A>G 
 p.Lys198Arg 
 De novo 
  
  
 GEN1196R046 
 missense_variant 
 c.538G>A 
 p.Glu180Lys 
 Unknown 
  
  
 GEN1196R047 
 missense_variant 
 c.238C>T 
 p.Arg80Cys 
 De novo 
  
 Simplex 
 GEN1196R048 
 missense_variant 
 c.479A>G 
 p.His160Arg 
 De novo 
  
 Simplex 
 GEN1196R049 
 missense_variant 
 c.149A>G 
 p.Tyr50Cys 
 De novo 
  
 Simplex 
 GEN1196R050 
 missense_variant 
 c.154G>A 
 p.Glu52Lys 
 De novo 
  
  
 GEN1196R051 
 missense_variant 
 c.149A>G 
 p.Tyr50Cys 
 De novo 
  
 Simplex 
 GEN1196R052 
 missense_variant 
 c.468T>A 
 p.Asp156Glu 
 De novo 
  
 Simplex 
 GEN1196R053 
 missense_variant 
 c.137G>T 
 p.Gly46Val 
 Familial 
 Maternal 
 Simplex 
 GEN1196R054 
 missense_variant 
 c.698T>C 
 p.Phe233Ser 
 De novo 
  
  

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
20
Deletion-Duplication
 33
 
20
Duplication
 1
 
20
Duplication
 1
 
20
Duplication
 1
 
20
Duplication
 3
 
20
Duplication
 1
 

Model Summary

The homozygous mutant Csnk2a1 mouse model with a missense mutation found in humans (K198R) shows embryonic lethality, while the heterozygote shows incomplete penetrance in the lethality phenotype, with surviving animals developing a smaller size. Heterozygous mutants show enlarged cerebral ventricles, decrease thickness of the corpus callosum and increased density of synapses in the hippocampus. The heterozygote mutants show deficiencies in hippocampus-dependent behaviors, including fear conditioning memory and spatial memory, and hippocampal long-term depression. The heterozygous mutants show no social phenotype but an increase in repetitive behaviors.

References

Type
Title
Author, Year
Primary
Missense mutation in the activation segment of the kinase CK2 models Okur-Chung neurodevelopmental disorder and alters the hippocampal glutamatergic synapse

M_CSNK2A1_1_KI_HM_K198R

Model Type: Genetic
Model Genotype: Homozygous
Mutation: Homozygous knockin mice carry two alleles with a K198R missense mutation in the Csnk2a1 gene (MGI:6383802).
Allele Type: ASD mutation
Strain of Origin: Not specified
Genetic Background: C57BL/6J
ES Cell Line: Not applicable
Mutant ES Cell Line:
Model Source: Jackson Laboratory

M_CSNK2A1_2_KI_HT_K198R

Model Type: Genetic
Model Genotype: Heterozygous
Mutation: Heterozygous knockin mice carry one allele with a K198R missense mutation in the Csnk2a1 gene (MGI:6383802).
Allele Type: ASD mutation
Strain of Origin: Not specified
Genetic Background: C57BL/6J
ES Cell Line: Not applicable
Mutant ES Cell Line:
Model Source: Jackson Laboratory

M_CSNK2A1_1_KI_HM_K198R

Category
Entity
Quantity
Experimental Paradigm
Age at Testing
Mortality/lethality: embryonic1
Increased
Description: Homozygous mutants show embryonic lethality.
 Genotypic ratio of progeny from heterozygous parents
 
Cardiovascular development and function: embryonic1
Decreased
Description: Homozygous mutant mice show edematous heart defects, the blood was not circulating, and the resorption of the yolk sac had started. At E11.5, homozygotes were non-viable, and 50% showed a failure to close the cranium.
 Macroscopic analysis
 E10.5-E11.5
 Not Reported:

M_CSNK2A1_2_KI_HT_K198R

Category
Entity
Quantity
Experimental Paradigm
Age at Testing
Rearing behavior2
Increased
Description: Heterozygous mice display enhanced stereotypies (rearings) which were assessed for 1 h during the dark active cycle (3â??4 am) cycle, with a similar result obtained during the light cycle.
 Home cage behavior
 
Morphology and size of the corpus callosum2
Decreased
Description: The thickness of the corpus callosum was reduced in heterozygous mutants.
 Histology
 
Synapse density2
Increased
Description: Synapse density was enhanced in heterozygous mice.
Exp Paradigm: hippocampus
 Electron microscopy
 
Size of cerebral ventricles: lateral ventricle2
Increased
Description: Lateral ventricle was enlarged in heterozygous mutants
 Histology
 
Post-synaptic density size2
Increased
Description: The thickness of the postsynaptic density is not changed, but postsynaptic density disc diameter was enhanced in heterozygous animals.
Exp Paradigm: hippocampus
 Electron microscopy
 
Synaptic plasticity: hippocampal LTP2
Decreased
Description: There is normal induction and expression of long-term potentiation (LTP) in the hippocampal slices prepared from wildtype mice, but an attenuation of LTP in slices from heterozygous mice.
Exp Paradigm: theta bust stimulation
 Field potential recordings
 
Repetitive digging2
Decreased
Description: Heterozygous mice showed impaired marble burying behavior compared to wildtype mice.
 Marble-burying test
 
Seizure threshold2
Decreased
Description: Heterozygous mice show an earlier onset of the seizure-preceding immobilization and seizures themselves.
Exp Paradigm: picrotoxin
 Observation of chemically induced seizures
 
Sensorimotor gating2
Decreased
Description: Heterozygous mice show a lower percentage of pre-pulse inhibition.
 Prepulse inhibition
 
Startle response: acoustic stimulus2
Decreased
Description: Heterozygous mice show a reduced startle response.
 Acoustic startle reflex test
 
Nest building behavior2
Decreased
Description: Heterozygous mice also exhibited a reduced nesting score.
 Nest building assay
 
Mortality/lethality: embryonic: incomplete penetrance1
Increased
Description: Heterozygous mutant mice are born at a lower-than-expected mendelian ratios.
 Genotypic ratio of progeny from heterozygous parents
 
Cardiovascular development and function: embryonic1
Decreased
Description: At E11.5, half of heterozygous embryos were viable and resembled wildtype, and others exhibited heart defects, were developmentally delayed and resembled homozygotes at E10.5.
 Macroscopic analysis
 E10.5-E11.5
Size/growth1
Decreased
Description: Male and female heterozygous mice weighed 16.07% and 17.6% less, respectively, at 14 weeks of age, a difference that increases with age for males reaching nearly 33.9% at 16 months.
 Body weight measurement
 
Mortality/lethality: life span: incomplete penetrance1
Decreased
Description: During aging, no difference was observed between sexes of the same genotypes, however heterozygous mice have significantly enhanced mortality rate.
 Survival analysis
 
Anxiety2
Decreased
Description: Heterozygous mice show decreased novelty-suppression.
 Novelty-suppressed feeding paradigm
 
Exploratory activity: habituation2
Decreased
Description: In their first 20 minutes of exposure to the open field environment, heterozygous mice are slightly hypoactive compared to wildtype.
 Open field test
 
Anxiety2
Decreased
Description: Heterozygous mice show increased time in the light box.
 Light-dark exploration test
 
Cued or contextual fear conditioning: memory of cue2
Decreased
Description: Heterozygous mice also observed a lower level of cue fear expression.
 Fear conditioning test
 
Cued or contextual fear conditioning: memory of context2
Decreased
Description: Heterozygous mice showed reduced fear expression 24 h after training, suggesting an impairment in contextual fear memory compared with wildtype mice.
 Fear conditioning test
 
Spatial working memory2
Decreased
Description: Heterozygous mice performed fewer correct alternations compared to wildtype.
Exp Paradigm: spontaneous alternation
 Y-maze test
 
Protein phosphorylation2
Abnormal
Description: Mass spectrometric analysis of striatal tissue revealed 13017 unique phosphopeptides (p-peptides), out of which 394 were significantly altered by a factor of 1.5 or more between genotypes. 163 were present at higher levels in wildtype striatum, while 231 peptides were enriched in heterozygous mice.
Exp Paradigm: striatum
 Mass spectrometry (MS)
 
Protein phosphorylation2
Decreased
Description: Heterozygous mutants show a 25% reduction of CK2 activity.
 Enzyme assay
 
Signaling: PI3K/AKT pathway2
Increased
Description: Heterozygous mutant mice show a significant decrease in phosphorylation of the CK2 site, Ser97. Heterozygote mice show a trend towards elevated phosphorylation of Ser473 AKT, a PDK1 substrate and an indicator of the activation state of AKT.
 Western blot
 
Signaling: mTOR pathway2
Increased
Description: S6 Ribosomal Protein S240/244 phosphorylation, a downstream readout of the mTOR pathway, is increased in heterozygotes.
 Western blot
 
Anxiety2
 No change
 Elevated plus maze test
 
Depression2
 No change
 Tail suspension test
 
Cognitive flexibility2
 No change
 Barnes maze test
 
Spatial learning2
 No change
 Barnes maze test
 
Spatial reference memory2
 No change
 Barnes maze test
 
Spatial reference memory2
 No change
 Y-maze test
 
Targeted expression2
 No change
 Immunohistochemistry
 
Targeted expression2
 No change
 Quantitative PCR (qRT-PCR)
 
Targeted expression2
 No change
 Western blot
 
Grip strength2
 No change
 Inverted grid test
 
Grip strength2
 No change
 Grip strength test
 
Motor coordination and balance2
 No change
 Accelerating rotarod test
 
Brain size2
 No change
 Macroscopic analysis
 
Neuronal number2
 No change
 Electron microscopy
 
Synaptic morphology2
 No change
 Electron microscopy
 
Social approach2
 No change
 Three-chamber social approach test
 
Social memory2
 No change
 Three-chamber social approach test
 
 Not Reported:

 

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