Alternative titles; symbols
HGNC Approved Gene Symbol: CSNK2A1
Cytogenetic location: 20p13 Genomic coordinates (GRCh38) : 20:472,498-543,790 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 20p13 | Okur-Chung neurodevelopmental syndrome | 617062 | Autosomal dominant | 3 |
CSNK2A1 encodes the alpha subunit of the heterodimeric casein kinase II protein, which is ubiquitously expressed and has an important role in cellular growth, proliferation, and apoptosis (summary by Chiu et al., 2018).
Casein kinase II is a serine/threonine kinase that phosphorylates acidic protein such as casein. It has a tetrameric a(2)/b(2) structure. The alpha subunit of molecular mass 40 kD possesses catalytic activity, whereas the beta subunit (115441), molecular mass 25 kD, is autophosphorylated in vitro. Meisner et al. (1989) reported the identification and nucleotide sequencing of a complete human cDNA for the alpha subunit. Using the full-length cDNA probe, Meisner et al. (1989) found 2 bands with restriction enzymes that have no recognition sites within the cDNA and 3 to 6 bands with enzymes having single internal sites. These results were considered consistent with the existence of 2 genes encoding alpha subunits. See 115442.
Wirkner et al. (1994) demonstrated that the CSNK2A1 gene contains 8 exons whose sequences comprise bases 102 to 824 of the coding region of the human casein kinase II alpha subunit. Three of the 9 introns are located at positions corresponding to those of the homologous gene in the nematode Caenorhabditis elegans. The introns contain 8 complete and 8 incomplete Alu repeats.
Phosphorylation of the human p53 protein (191170) at ser392 is responsive to ultraviolet (UV) but not gamma irradiation. Keller et al. (2001) identified and purified a mammalian UV-activated protein kinase complex that phosphorylates ser392 in vitro. This kinase complex contains CK2 and the chromatin transcriptional elongation factor FACT, a heterodimer of SPT16 (605012) and SSRP1 (604328). In vitro studies showed that FACT alters the specificity of CK2 in the complex such that it selectively phosphorylates p53 over other substrates, including casein. In addition, phosphorylation by the kinase complex was found to enhance p53 activity. These results provided a potential mechanism for p53 activation by UV irradiation.
Doray et al. (2002) demonstrated that the Golgi-localized, gamma-ear-containing adenosine diphosphate ribosylation factor-binding proteins (GGA1, 606004 and GGA3, 606006) and the coat protein adaptor protein-1 (AP-1) complex (see AP1G2, 603534) colocalize in clathrin-coated buds of the trans-Golgi networks of mouse L cells and human HeLa cells. Binding studies revealed a direct interaction between the hinge domains of the GGAs and the gamma-ear domain of AP-1. Further, AP-1 contained bound casein kinase-2 that phosphorylated GGA1 and GGA3, thereby causing autoinhibition. Doray et al. (2002) demonstrated that this autoinhibition could induce the directed transfer of mannose 6-phosphate receptors (see 154540) from the GGAs to AP-1. Mannose 6-phosphate receptors that were defective in binding to GGAs were poorly incorporated into adaptor protein complex containing clathrin coated vesicles. Thus, Doray et al. (2002) concluded that GGAs and the AP-1 complex interact to package mannose 6-phosphate receptors into AP-1-containing coated vesicles.
Lin et al. (2002) identified a Drosophila circadian mutant, Timekeeper (Tik), that behaved in a dominant manner. Tik homozygotes do not live to adulthood, and heterozygotes have a circadian rhythm lengthened by about 3 hours. Lin et al. (2002) showed that the catalytic subunit of Drosophila casein kinase-2 (CK2-alpha) is expressed predominantly in the cytoplasm of key circadian pacemaker neurons. CK2-alpha mutant flies showed lengthened circadian period, decreased CK2 activity, and delayed nuclear entry of Per (see 602260). Lin et al. (2002) suggested that these are probably direct, as CK2-alpha specifically phosphorylates Per in vitro. Lin et al. (2002) proposed that CK2 is an evolutionary link between the divergent circadian systems of animals, plants, and fungi.
Loizou et al. (2004) showed that CK2 phosphorylates the scaffold protein XRCC1 (194360) and thereby enables the assembly and activity of DNA single-strand break repair protein complexes in vitro and at sites of chromosome breakage. Inhibition of XRCC1 phosphorylation by mutation of the CK2 phosphorylation sites or by preventing CK2 activity using a highly specific inhibitor ablated the rapid repair of cellular DNA single-strand breaks by XRCC1. These data identified a direct role for CK2 in the repair of chromosome DNA strand breaks and in maintaining genetic integrity.
Downstream core promoter elements (DPE) are regulatory sequences that add diversity to the promoter architecture of RNA polymerase II-transcribed genes. Despite a functional correlation between the presence of TFIID (313650) and DPE, Lewis et al. (2005) found that TFIID was insufficient for DPE-specific transcription in HeLa cells. Using a functional transcription assay coupled with conventional biochemistry, they found that protein kinase CK2, in conjunction with the coactivator PC4 (600503), established DPE-specific transcription.
By segregation analysis of rodent-human somatic cell hybrids and chromosomal in situ hybridization, Yang-Feng et al. (1991) identified 2 loci for the alpha subunit of casein kinase II: 11p15.5-p.15.4 and 20p13. Whether one of these is a pseudogene remained to be determined. Boldyreff et al. (1992) likewise found 2 assignments by in situ hybridization: 11pter-p15.1 and 20p13. Only the locus on chromosome 11 was confirmed by somatic cell hybrid analysis, based on the presence of a CK2A1-specific 20-kb fragment. However, Wirkner et al. (1992) demonstrated that the sequence that maps to 11p15 by in situ hybridization has the characteristics of a processed pseudogene.
By fluorescence in situ hybridization using an 18.9-kb genomic clone representing the central portion of the gene, Wirkner et al. (1994) mapped CSNK2A1 to 20p13. Using the genomic clone, no hybridization signal was obtained in 11p15 as had previously been the case when the cDNA was used as probe (Yang-Feng et al., 1991).
In 5 unrelated girls with Okur-Chung neurodevelopmental syndrome (OCNDS; 617062), Okur et al. (2016) identified de novo heterozygous mutations in the CSNK2A1 gene (115440.0001-115440.0005), including 4 missense mutations and 1 splice site mutation. Functional studies of the variants and studies of patient cells were not performed, but Okur et al. (2016) noted that the CSNK2A1 gene is expressed in the brain and encodes the catalytic subunit of protein kinase CK2, which is involved in many biologic processes. The mutations were found by whole-exome sequencing of 4,102 patients with developmental delay/intellectual disability.
In a 7-year-old German boy with OCNDS, Trinh et al. (2017) identified a de novo heterozygous missense mutation (D156H; 115440.0006) in the CSNK2A1 gene. The mutation was identified by trio exome sequencing and confirmed by Sanger sequencing.
Chiu et al. (2018) summarized data on 16 de novo heterozygous mutations in the CSNK2A1 gene that had been identified in 22 patients with OCNDS, including their 8 newly reported patients. All but 2 mutations were located in the large protein kinase domain that spans exons 4 to 12. Most of the mutations occurred in exon 9, including the most frequently observed mutation, K198R (115440.0002), which was found in 5 patients. The mutations were believed to be disruptive by altering highly conserved amino acids with important roles in stabilization and substrate recognition.
Among 11 patients with OCNDS from the DDD study, Owen et al. (2018) identified 8 different de novo heterozygous missense mutations, including the recurrent K198R mutation, which was found in 4 unrelated individuals, leading the authors to suggested that this is a mutation hotspot. None of the mutations were found in the gnomAD database.
In a 13-year-old girl (patient 4) with Okur-Chung neurodevelopmental syndrome (OCNDS; 617062), Okur et al. (2016) identified a de novo heterozygous T-to-C transition (c.824+2T-C) in intron 10 of the CSNK2A1 gene, predicted to result in a splice site variant. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was not found in the 1000 Genomes Project, Exome Variant Server, or ExAC databases, or in 24,578 in-house control exomes. Functional studies of the variant and studies of patient cells were not performed.
In a 4.5-year-old girl (patient 2) with Okur-Chung neurodevelopmental syndrome (OCNDS; 617062), Okur et al. (2016) identified a de novo heterozygous c.593A-G transition in the CSNK2A1 gene, resulting in a lys198-to-arg (K198R) substitution in the highly conserved activation domain. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was not found in the 1000 Genomes Project, Exome Variant Server, or ExAC databases, or in 24,578 in-house control exomes. Functional studies of the variant and studies of patient cells were not performed.
Chiu et al. (2018) summarized data on 16 de novo heterozygous CSNK2A1 mutations that had been reported in 22 patients with OCNDS, including their 8 newly reported patients, and found that K198R was the most common mutation, occurring in 5 patients.
Four of the 8 de novo heterozygous missense mutations in CSNK2A1 identified by Owen et al. (2018) in patients with OCNDS were K198R, leading the authors to propose that this is a mutation hotspot.
Akahira-Azuma et al. (2018) identified de novo heterozygosity for the recurrent K198R mutation in the CSNK2A1 gene in an 8-year-old Japanese boy with OCNDS.
In a 4-year-old girl (patient 3) with Okur-Chung neurodevelopmental syndrome (OCNDS; 617062), Okur et al. (2016) identified a de novo heterozygous c.524A-G transition in the CSNK2A1 gene, resulting in an asp175-to-gly (D175G) substitution in the highly conserved activation domain. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was not found in the 1000 Genomes Project, Exome Variant Server, or ExAC databases, or in 24,578 in-house control exomes. Functional studies of the variant and studies of patient cells were not performed.
In a 2-year-old girl (patient 5) with Okur-Chung neurodevelopmental syndrome (OCNDS; 617062), Okur et al. (2016) identified a de novo heterozygous c.149A-C transversion in the CSNK2A1 gene, resulting in a tyr50-to-ser (Y50S) substitution in the highly conserved ATP/GTP binding loop. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was not found in the 1000 Genomes Project, Exome Variant Server, or ExAC databases, or in 24,578 in-house control exomes. Functional studies of the variant and studies of patient cells were not performed.
In a 6-year-old girl (patient 1) with Okur-Chung neurodevelopmental syndrome (OCNDS; 617062), Okur et al. (2016) identified a de novo heterozygous c.140G-A transition in the CSNK2A1 gene, resulting in an arg47-to-gln (R47Q) substitution in the highly conserved ATP/GTP binding loop. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was not found in the 1000 Genomes Project, Exome Variant Server, or ExAC databases, or in 24,578 in-house control exomes. Functional studies of the variant and studies of patient cells were not performed.
In a 7-year-old German boy with Okur-Chung neurodevelopmental syndrome (OCNDS; 617062), Trinh et al. (2017) identified a do novo heterozygous c.466G-C transversion (chr20.476407, GRCh37) in the CSNK2A1 gene, resulting in an asp156-to-his (D156H) substitution. The mutation was found by trio exome sequencing and confirmed by Sanger sequencing.
In a 2.5-year-old girl with Okur-Chung neurodevelopmental syndrome (OCNDS; 617062), Chiu et al. (2018) identified a de novo heterozygous c.1A-G transition (c.1A-G, NM_177559.2) in the CSNK2A2 gene, resulting in a met1-to-val (M1V) substitution. The mutation was predicted to lead to a loss of amino acids 1 to 137, the position of the next in-frame start codon.
Akahira-Azuma, M., Tsurusaki, Y., Enomoto, Y., Mitsui, J., Kurosawa, K. Refining the clinical phenotype of Okur-Chung neurodevelopmental syndrome. Hum. Genome Var. 5: 18011, 2018. Note: Electronic Article. [PubMed: 29619237] [Full Text: https://doi.org/10.1038/hgv.2018.11]
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Keller, D. M., Zeng, X., Wang, Y., Zhang, Q. H., Kapoor, M., Shu, H., Goodman, R., Lozano, G., Zhao, Y., Lu, H. A DNA damage-induced p53 serine 392 kinase complex contains CK2, hSpt16, and SSRP1. Molec. Cell 7: 283-292, 2001. [PubMed: 11239457] [Full Text: https://doi.org/10.1016/s1097-2765(01)00176-9]
Lewis, B. A., Sims, R. J., III, Lane, W. S., Reinberg, D. Functional characterization of core promoter elements: DPE-specific transcription requires the protein kinase CK2 and the PC4 coactivator. Molec. Cell 18: 471-481, 2005. [PubMed: 15893730] [Full Text: https://doi.org/10.1016/j.molcel.2005.04.005]
Lin, J.-M., Kilman, V. L., Keegan, K., Paddock, B., Emery-Le, M., Rosbash, M., Allada, R. A role for casein kinase 2-alpha in the Drosophila circadian clock. Nature 420: 816-820, 2002. [PubMed: 12447397] [Full Text: https://doi.org/10.1038/nature01235]
Loizou, J. I., El-Khamisy, S. F., Zlatanou, A., Moore, D. J., Chan, D. W., Qin, J., Sarno, S., Meggio, F., Pinna, L. A., Caldecott, K. W. The protein kinase CK2 facilitates repair of chromosomal DNA single-strand breaks. Cell 117: 17-28, 2004. [PubMed: 15066279] [Full Text: https://doi.org/10.1016/s0092-8674(04)00206-5]
Meisner, H., Heller-Harrison, R., Buxton, J., Czech, M. P. Molecular cloning of the human casein kinase II alpha subunit. Biochemistry 28: 4072-4076, 1989. Note: Erratum: Biochemistry 28: 7138 only, 1989. [PubMed: 2752008] [Full Text: https://doi.org/10.1021/bi00435a066]
Okur, V., Cho, M. T., Henderson, L., Retterer, K., Schneider, M., Sattler, S., Niyazov, D., Azage, M., Smith, S., Picker, J., Lincoln, S., Tarnopolsky M., Brady, L., Bjornsson, H. T., Applegate, C., Dameron, A., Willaert, R., Baskin, B., Juusola, J., Chung, W. K. De novo mutations in CSNK2A1 are associated with neurodevelopmental abnormalities and dysmorphic features. Hum. Genet. 135: 699-705, 2016. [PubMed: 27048600] [Full Text: https://doi.org/10.1007/s00439-016-1661-y]
Owen, C. I., Bowden, R., Parker, M. J., Patterson, M. J., Patterson, J., Price, S., Sarkar, A., Castle, B., Deshpande, C., Splitt, M., Ghali, N., Dean, J., Green, A. J., Crosby, D., Deciphering Developmental Disorders Study, Tatton-Brown, K. Extending the phenotype associated with the CSNK2A1-related Okur-Chung syndrome--a clinical study of 11 individuals. Am. J. Med. Genet. 176A: 1108-1114, 2018. [PubMed: 29383814] [Full Text: https://doi.org/10.1002/ajmg.a.38610]
Trinh, J., Huning, I., Budler, N., Hingst, V., Lohmann, K., Gillessen-Kaesbach, G. A novel de novo mutation in CSNK2A1: reinforcing the link to neurodevelopmental abnormalities and dysmorphic features. J. Hum. Genet. 62: 1005-1006, 2017. [PubMed: 28725024] [Full Text: https://doi.org/10.1038/jhg.2017.73]
Wirkner, U., Voss, H., Lichter, P., Ansorge, W., Pyerin, W. The human gene (CSNK2A1) coding for the casein kinase II subunit alpha is located on chromosome 20 and contains tandemly arranged Alu repeats. Genomics 19: 257-265, 1994. [PubMed: 8188256] [Full Text: https://doi.org/10.1006/geno.1994.1056]
Wirkner, U., Voss, H., Lichter, P., Weitz, S., Ansorge, W., Pyerin, W. Human casein kinase II subunit alpha: sequence of a processed (pseudo)gene and its localization on chromosome 11. Biochim. Biophys. Acta 1131: 220-222, 1992. [PubMed: 1610905] [Full Text: https://doi.org/10.1016/0167-4781(92)90083-c]
Yang-Feng, T. L., Zheng, K., Kopatz, I., Naiman, T., Canaani, D. Mapping of the human casein kinase II catalytic subunit genes: two loci carrying the homologous sequences for the alpha subunit. Nucleic Acids Res. 19: 7125-7129, 1991. [PubMed: 1766873] [Full Text: https://doi.org/10.1093/nar/19.25.7125]