Skip to main content

Advertisement

Log in

De novo mutations in CSNK2A1 are associated with neurodevelopmental abnormalities and dysmorphic features

  • Original Investigation
  • Published:
Human Genetics Aims and scope Submit manuscript

Abstract

Whole exome sequencing (WES) can be used to efficiently identify de novo genetic variants associated with genetically heterogeneous conditions including intellectual disabilities. We have performed WES for 4102 (1847 female; 2255 male) intellectual disability/developmental delay cases and we report five patients with a neurodevelopmental disorder associated with developmental delay, intellectual disability, behavioral problems, hypotonia, speech problems, microcephaly, pachygyria and dysmorphic features in whom we have identified de novo missense and canonical splice site mutations in CSNK2A1, the gene encoding CK2α, the catalytic subunit of protein kinase CK2, a ubiquitous serine/threonine kinase composed of two regulatory (β) and two catalytic (α and/or α′) subunits. Somatic mutations in CSNK2A1 have been implicated in various cancers; however, this is the first study to describe a human condition associated with germline mutations in any of the CK2 subunits.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491:56–65. doi:10.1038/nature11632

    Article  PubMed  Google Scholar 

  • Baier A, Alikowska E, Szyszka R (2015) Yeast Asf1 protein as modulator of protein kinase CK2 activity. In: Ahmed K, Issinger OG, Szyszka R (eds) Protein kinase CK2 cellular function in normal and disease states, vol 12. Springer, e-book

  • Benveniste EN, Gray GK, McFarland BC (2015) Protein kinase CK2 and dysregulated oncogenic inflammatory signaling pathways. In: Ahmed K, Issinger OG, Szyszka R (eds) Protein kinase CK2 cellular function in normal and disease states, vol 12. Springer, e-book

  • Ceglia I, Flajolet M, Rebholz H (2011) Predominance of CK2alpha over CK2alpha′ in the mammalian brain. Mol Cell Biochem 356:169–175. doi:10.1007/s11010-011-0963-6

    Article  CAS  PubMed  Google Scholar 

  • Dominguez I, Degano IR, Chea K, Cha J, Toselli P, Seldin DC (2011) CK2alpha is essential for embryonic morphogenesis. Mol Cell Biochem 356:209–216. doi:10.1007/s11010-011-0961-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H, Ding M, Bamford S, Cole C, Ward S, Kok CY, Jia M, De T, Teague JW, Stratton MR, McDermott U, Campbell PJ (2015) COSMIC: exploring the world’s knowledge of somatic mutations in human cancer. Nucleic Acids Res 43:D805–D811. doi:10.1093/nar/gku1075

    Article  PubMed  Google Scholar 

  • Ku CS, Polychronakos C, Tan EK, Naidoo N, Pawitan Y, Roukos DH, Mort M, Cooper DN (2013) A new paradigm emerges from the study of de novo mutations in the context of neurodevelopmental disease. Mol Psychiatry 18:141–153. doi:10.1038/mp.2012.58

    Article  CAS  PubMed  Google Scholar 

  • Landesman-Bollag E, Belkina A, Hovey B, Connors E, Cox C, Seldin DC (2011) Developmental and growth defects in mice with combined deficiency of CK2 catalytic genes. Mol Cell Biochem 356:227–231. doi:10.1007/s11010-011-0967-2

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lolli G, Pinna LA, Battistutta R (2012) Structural determinants of protein kinase CK2 regulation by autoinhibitory polymerization. ACS Chem Biol 7:1158–1163. doi:10.1021/cb300054n

    Article  CAS  PubMed  Google Scholar 

  • Lolli G, Ranchio A, Battistutta R (2014) Active form of the protein kinase CK2 alpha2beta2 holoenzyme is a strong complex with symmetric architecture. ACS Chem Biol 9:366–371. doi:10.1021/cb400771y

    Article  CAS  PubMed  Google Scholar 

  • Lou DY, Dominguez I, Toselli P, Landesman-Bollag E, O’Brien C, Seldin DC (2008) The alpha catalytic subunit of protein kinase CK2 is required for mouse embryonic development. Mol Cell Biol 28:131–139. doi:10.1128/MCB.01119-07

    Article  CAS  PubMed  Google Scholar 

  • Niefind K, Issinger OG (2010) Conformational plasticity of the catalytic subunit of protein kinase CK2 and its consequences for regulation and drug design. Biochim Biophys Acta 1804:484–492. doi:10.1016/j.bbapap.2009.09.022

    Article  CAS  PubMed  Google Scholar 

  • Niefind K, Guerra B, Ermakowa I, Issinger OG (2001) Crystal structure of human protein kinase CK2: insights into basic properties of the CK2 holoenzyme. EMBO J 20:5320–5331. doi:10.1093/emboj/20.19.5320

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sarno S, Vaglio P, Meggio F, Issinger OG, Pinna LA (1996) Protein kinase CK2 mutants defective in substrate recognition. Purification and kinetic analysis. J Biol Chem 271:10595–10601

    Article  CAS  PubMed  Google Scholar 

  • Sarno S, Vaglio P, Marin O, Meggio F, Issinger OG, Pinna LA (1997) Basic residues in the 74–83 and 191–198 segments of protein kinase CK2 catalytic subunit are implicated in negative but not in positive regulation by the beta-subunit. Eur J Biochem 248:290–295

    Article  CAS  PubMed  Google Scholar 

  • Seldin DC, Lou DY, Toselli P, Landesman-Bollag E, Dominguez I (2008) Gene targeting of CK2 catalytic subunits. Mol Cell Biochem 316:141–147. doi:10.1007/s11010-008-9811-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Soden SE, Saunders CJ, Willig LK, Farrow EG, Smith LD, Petrikin JE, LePichon JB, Miller NA, Thiffault I, Dinwiddie DL, Twist G, Noll A, Heese BA, Zellmer L, Atherton AM, Abdelmoity AT, Safina N, Nyp SS, Zuccarelli B, Larson IA, Modrcin A, Herd S, Creed M, Ye Z, Yuan X, Brodsky RA, Kingsmore SF (2014) Effectiveness of exome and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders. Sci Transl Med 6:265ra168. doi:10.1126/scitranslmed.3010076

  • St-Denis NA, Litchfield DW (2009) Protein kinase CK2 in health and disease: from birth to death: the role of protein kinase CK2 in the regulation of cell proliferation and survival. Cell Mol Life Sci 66:1817–1829. doi:10.1007/s00018-009-9150-2

    Article  CAS  PubMed  Google Scholar 

  • Tanaka AJ, Cho MT, Millan F, Juusola J, Retterer K, Joshi C, Niyazov D, Garnica A, Gratz E, Deardorff M, Wilkins A, Ortiz-Gonzalez X, Mathews K, Panzer K, Brilstra E, van Gassen KL, Volker-Touw CM, van Binsbergen E, Sobreira N, Hamosh A, McKnight D, Monaghan KG, Chung WK (2015) Mutations in SPATA5 are associated with microcephaly, intellectual disability, seizures, and hearing loss. Am J Hum Genet 97:457–464. doi:10.1016/j.ajhg.2015.07.014

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wirkner U, Voss H, Ansorge W, Pyerin W (1998) Genomic organization and promoter identification of the human protein kinase CK2 catalytic subunit alpha (CSNK2A1). Genomics 48:71–78. doi:10.1006/geno.1997.5136

    Article  CAS  PubMed  Google Scholar 

  • Zheng Y, McFarland BC, Drygin D, Yu H, Bellis SL, Kim H, Bredel M, Benveniste EN (2013) Targeting protein kinase CK2 suppresses prosurvival signaling pathways and growth of glioblastoma. Clin Cancer Res 19:6484–6494. doi:10.1158/1078-0432.ccr-13-0265

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

We thank the families for their generous contribution. This work was supported in part by a Grant from the Simons Foundation.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Wendy K. Chung.

Ethics declarations

Conflict of interest

Megan Cho, Lindsay Henderson, Kyle Retterer, Amy Dameron, Rebecca Willaert, Berivan Baskin, and Jane Juusola are employees of GeneDx. Wendy Chung is a consultant to BioReference Laboratories.

Additional information

Data deposition and access: These CSNK2A1 variants have been deposited in ClinVar.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Okur, V., Cho, M.T., Henderson, L. et al. De novo mutations in CSNK2A1 are associated with neurodevelopmental abnormalities and dysmorphic features. Hum Genet 135, 699–705 (2016). https://doi.org/10.1007/s00439-016-1661-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00439-016-1661-y

Keywords

Navigation