Research Explained: Identification and functional analysis of a novel CSNK2A1 frameshift variant in stillbirth
Zhang, N. et al.
2025
Research Explained by: Lindsay Bass, CSNK2A1 Foundation Intern
Edited by: Gabrielle Rushing, PhD, CSNK2A1 Foundation Chief Scientific Officer
Reviewed by Parent Advisory Board members
Content warning: stillbirth
Protein kinase CK2 is expressed in all cell types. As a kinase, it adds a small chemical tag called a phosphate to a protein to impact the protein’s function. CK2 is composed of two activating (CK2α, CK2α’) and two regulatory subunits (CK2β). CK2α is encoded by the gene CSNK2A1, which is highly expressed in the brain. Mutations in CSNK2A1 are associated with Okur-Chung neurodevelopmental syndrome (OCNDS), and mutations/variants can be found along the various functional regions of CSNK2A1.
In this study, a novel mutation in CSNK2A1 was identified in a stillbirth case. A 33-year-old pregnant woman with unremarkable pregnancy history and a non-related partner showed abnormal results on a fetal ultrasound, including abnormalities of the brain and heart. Stillbirth occurred at 35 weeks. Whole genome sequencing was performed on the fetus, and a new frameshift mutation on exon 13 of CSNK2A1 was identified, c.1020_1021delAG (p.Gly342Glnfs*57). In this case, a deletion of two nucleotides from the DNA sequence (at positions 1020 and 1021) shifts the pattern by which the DNA sequence instructs the subsequent amino acid sequence. This changes the remaining protein sequence following the deletions. This frameshift mutation is distinct from most mutations in CSNK2A1, which are missense mutations that alter a single amino acid. No variants in other genes involved in fetal development were identified. The variant was heterozygous in the fetus but absent in both parents. The variant was located outside functional regions of the protein and was classified as a variant of uncertain significance (VUS), meaning that current evidence is insufficient to determine whether the variant is disease-causing or harmless. Alignment of the variant and wildtype (usual) structures showed that the frameshift mutation replaced the original end of the protein with a novel protein sequence that was six amino acids longer and had a distinct coiled structure.
To assess the functional consequences of this mutation, wildtype and variant CK2α protein were expressed in a human neuroblastoma cell line. Kinase activity of the cells expressing the variant CK2α protein (variant cells) did not differ from the cells expressing wildtype CK2α protein (wildtype cells). Since the kinase function of the protein did not differ between wildtype and variant CK2α, the researchers asked whether the amount of protein differed. The variant cells expressed significantly more mRNA, but significantly less protein than the wildtype cells. Normally, the amount of mRNA correlates with the amount of protein produced. The disconnect between levels of mRNA and protein could be explained by an impairment in the ability to make the protein or increased breakdown of the protein. Cells can add a molecule called ubiquitin to proteins to tag them for breakdown (or degradation). This process is called ubiquitination. Here, the variant cells express higher levels of ubiquitinated CK2α protein, suggesting increased CK2α protein degradation. These findings suggest increased degradation of the mutant CK2α, rather than impaired kinase activity, may lead to the potentially pathogenic impact of this frameshift mutation.
Glossary
Amino acid: the building block of a protein.
c.1020_1021delAG (p.Gly342Glnfs*57): A genetic mutation where the nucleotides adenine (A) and guanine (G) are deleted from positions 1020 and 1021 of the DNA sequence. This frameshift mutation (fs, see definition) changes amino acid (see definition) glycine (Gly) to glutamine (Gln) at position 342 and impacts the remaining protein sequence, which ends 57 amino acids after the frameshift mutation.
Exon: region of DNA that instructs protein production.
Frameshift mutation: an addition or deletion of nucleotide(s) that can change the pattern in which the remaining DNA instructions are read and lead to production of a completely different region of protein.
Heterozygous: expressed in only one copy of the gene. Humans typically have two copies of each gene, one from each parent.
mRNA: a nucleotide sequence that carries genetic instructions from DNA and serves as a template to create proteins.
Neuroblastoma cell line: human cells used for research that were developed from neuron cancer cells. Cell lines are ideal for research because they can be grown continually. CSNK2A1 is expressed in neurons, making this a good model to study the functional consequences of this new mutation.
Pathogenic: describes a gene change that is known to cause disease. It means the variant disrupts normal biological function and leads to health problems.
Stillbirth: A stillbirth is the loss of a baby before birth, usually after 20 weeks of pregnancy. The baby shows no signs of life at delivery, such as breathing, movement, or a heartbeat.
Whole genome sequencing: a research technique that reads a person’s complete DNA sequence (genetic instructions). It can determine if there are any changes from normal which may explain a given medical condition.
Wildtype: the normal version of a gene, protein or organism (often compared to a mutated or modified version).