Summary
In this study, the functional implications of CSNK2A1 haploinsufficiency in human disease were analyzed by examining clinical phenotypes and performing functional studies on patients carrying loss-of-function mutations. The evidence was derived from two patients: Patient 1 with a missense variant (CSNK2A1 NM_177559.2:c.593A>G, p.(Lys198Arg)) and Patient 2 with a nonsense mutation (CSNK2A1 NM_177559.2:c.571C>T, p.Arg191*). Patient 1 exhibited a clinical phenotype including global developmental delays, hypotonia, intractable seizures, and additional severe manifestations such as respiratory failure, without inheritance information available. Patient 2 presented with a phenotype resembling Dravet syndrome, similarly showing global developmental delays and intractable seizures, and deceased at 1 year and 7 months; inheritance was tested but the transmission pattern is not specified. Functional studies employing HEK293T cells elucidated the interaction between CSNK2A1 and CSNK2B proteins, with one variant showing no interaction, suggesting a role in CK2 holoenzyme instability. Another study indicated a wild type and a specific mutant CSNK2B interaction comparable to CSNK2A1, implying the variant does not impact the interaction. These cellular analyses, alongside discussions on the functional impact on CK2α, supported the gene-disease association related to CSNK2A1 haploinsufficiency.
Evidence of Haploinsufficiency
Patient Identifier: Patient 1
Mutation Type: missense variant
Mutation Details: CSNK2A1 (NM_177559.2:c.593A>G, p.(Lys198Arg))
Clinical Phenotype: Global developmental delays, hypotonia, intractable seizures, facial dysmorphisms, brain abnormalities, short stature, congenital biliary dilatation, pharyngeal dysphagia, easy fatigability and muscle weakness, gait difficulty, respiratory failure
Inheritance Tested: No
Effect on Gene Function: The variant in CSNK2A1 was classified as pathogenic.
Direct Quote: "Two patients with CSNK2A1 variants shared global developmental delays, hypotonia, and intractable seizures, but each exhibited interesting features. Patient 1 showed...distinct easy fatigability and muscle weakness. These manifestations progressively worsened and led to gait difficulty and respiratory failure."
Location in Paper: Results Clinical features
Patient Identifier: Patient 2
Mutation Type: nonsense mutation
Mutation Details: CSNK2A1 variant (NM_177559.2:c.571C>T, p.Arg191*)
Clinical Phenotype: Global developmental delays, hypotonia, intractable seizures, resembling those with Dravet syndrome, died from acute encephalopathy at 1 year and 7 months, no dysmorphic features or brain abnormalities noted
Inheritance Tested: Yes
Effect on Gene Function: The p.Arg191* mutation is classified as pathogenic and is likely to cause truncated protein which leads to loss of function.
Direct Quote: "Two patients with CSNK2A1 variants shared global developmental delays, hypotonia, and intractable seizures, but each exhibited interesting features. Meanwhile, patient 2 presented a severer course, with seizures resembling those with Dravet syndrome... identified a novel CSNK2A1 variant (NM_177559.2:c.571C>T, p.Arg191*)... In accordance with the ACMG guideline, CSNK2A1 (c.571C>T) variant was classified as pathogenic."
Location in Paper: Results Clinical features, Main text
Clinical Features
Feature: developmental delay
Frequency: 28/28
Direct Quote: "The most general findings were developmental delay (28/28), intellectual disabilities (26/28), and hypotonia (20/28)."
Location in Paper: Discussion
Feature: intellectual disabilities
Frequency: 26/28
Direct Quote: "The most general findings were developmental delay (28/28), intellectual disabilities (26/28), and hypotonia (20/28)."
Location in Paper: Discussion
Feature: hypotonia
Frequency: 20/28
Direct Quote: "The most general findings were developmental delay (28/28), intellectual disabilities (26/28), and hypotonia (20/28)."
Location in Paper: Discussion
Functional Studies
Study Type: Cell culture and molecular studies
Methodology: Mutant HA-tagged CSNK2B vectors with/without FLAG-tagged CSNK2A1 vectors were transfected in HEK293T cells, followed by immunoprecipitation and western blotting analysis.
Conclusions: The study revealed that the impact on CSNK2A1 function could be identified through molecular studies, but specifics were not provided.
Direct Quote: "Cell culture, transfection, immunoprecipitation, and western blotting"
Location in Paper: Plasmid construction and Cell culture, transfection, immunoprecipitation, and western blotting sections
Study Type: Functional protein analysis
Methodology: Western blots using extracts from HEK293T cells and co-immunoprecipitation (co-IP) assay to examine the interaction between CSNK2A1 and WT or mutant CSNK2B proteins.
Conclusions: p.His165Arg mutant CSNK2B showed comparable interaction to the CSNK2A1 protein, suggesting that at least for the CSNK2B variant, there is no impact on interaction with CSNK2A1; implications for CSNK2A1 haploinsufficiency are not directly addressed.
Direct Quote: "using co-IP assay we examined the protein interaction between the CSNK2A1 and WT or mutant CSNK2B proteins. The three independent co-IP experiments indicated that wild type and p.His165Arg mutant CSNK2B showed comparable interaction to the CSNK2A1 protein."
Location in Paper: Main text
Study Type: In vivo protein degradation and co-IP assay
Methodology: Examining protein interaction between CSNK2A1 and WT or mutant CSNK2B proteins
Conclusions: p.Pro179Tyrfs*49 mutant CSNK2B showed no interaction with the CSNK2A1, which may induce the instability of the protein structure of CK2 holoenzyme
Direct Quote: "Next, using co-IP assay we examined the protein interaction between the CSNK2A1 and WT or mutant CSNK2B proteins. ... p.Pro179Tyrfs*49 mutant CSNK2B showed no interaction with the CSNK2A1 (Fig. 3d). These findings suggested that p.Pro179Tyrfs*49 mutant may lack the binding ability with CSNK2A1, which may induce the instability of the protein structure of the CK2 holoenzyme."
Location in Paper: Results
Study Type: Analysis of CK2α functional impact
Methodology: Inspection of muscle pathology and nerve conduction studies; discussion of previously known functions of CK2; analysis of phenotypes among patients with missense hotspot variant p.Lys198Arg
Conclusions: Variants in CSNK2A1 might have dominant-negative effects on CK2α function, but functional confirmation by molecular biological methods is indispensable
Direct Quote: "These findings imply CK2 may play important roles in the muscular nerve transmission mechanism and loss-of-CK2 function may be involved in the pathogenesis of muscle weakness; however, the examination of myopathology and repeatedly stimulated nerve conduction studies in patient 1 showed no evident abnormal findings. The impact of CKα functional disability in the signal transduction at NMJ was still uncertain; therefore, further research is needed to prove the relevance of variants in CSNK2A1 in muscle weakness."
Location in Paper: discussion of the functional impact of CSNK2A1 variants