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Novel calcineurin A (PPP3CA) variant associated with epilepsy, constitutive enzyme activation and downregulation of protein expression


PPP3CA encodes calmodulin-binding catalytic subunit of calcineurin, a ubiquitously expressed calcium/calmodulin-regulated protein phosphatase. Recently de novo PPP3CA variants were reported as a cause of disease in 12 subjects presenting with epileptic encephalopathy and dysmorphic features. We describe a boy with similar phenotype and severe early onset epileptic encephalopathy in whom a novel de novo c.1324C>T (p.(Gln442Ter)) PPP3CA variant was found by whole exome sequencing. Western blot experiments in patient’s cells (EBV transformed lymphocytes and neuronal cells derived through reprogramming) indicate that despite normal mRNA abundance the protein expression level is strongly reduced both for the mutated and wild-type protein. By in vitro studies with recombinant protein expressed in E. coli we show that c.1324C>T (p.(Gln442Ter)) results in constitutive activation of the enzyme. Our results confirm the role of PPP3CA defects in pathogenesis of a distinct neurodevelopmental disorder including severe epilepsy and dysmorphism and provide further functional clues regarding the pathogenic mechanism.

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We thank Dr. Ralf Kühn (Max-Delbrück-Centrum für Molekulare Medizin) and Dr. Heiko Lickert (Helmholtz Center Munich) for kindly providing the control iPSC line XM001. This work was supported by the National Science Centre (NCN) Poland, Grants 2013/11/B/NZ7/04944 (RP), 2014/13/B/NZ3/02947 (MDz), and 2016/22/M/NZ2/00548 (PL).

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The authors declare that they have no conflict of interest.

Correspondence to Rafał Płoski.

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