De Novo Mutations in PPP3CA Cause Severe Neurodevelopmental Disease with Seizures

Abstract

Exome sequencing has readily enabled the discovery of the genetic mutations responsible for a wide range of diseases. This success has been particularly remarkable in the severe epilepsies and other neurodevelopmental diseases for which rare, often de novo, mutations play a significant role in disease risk. Despite significant progress, the high genetic heterogeneity of these disorders often requires large sample sizes to identify a critical mass of individuals with disease-causing mutations in a single gene. By pooling genetic findings across multiple studies, we have identified six individuals with severe developmental delay (6/6), refractory seizures (5/6), and similar dysmorphic features (3/6), each harboring a de novo mutation in PPP3CA. PPP3CA encodes the alpha isoform of a subunit of calcineurin. Calcineurin encodes a calcium- and calmodulin-dependent serine/threonine protein phosphatase that plays a role in a wide range of biological processes, including being a key regulator of synaptic vesicle recycling at nerve terminals. Five individuals with de novo PPP3CA mutations were identified among 4,760 trio probands with neurodevelopmental diseases; this is highly unlikely to occur by chance (p = 1.2 × 10) given the size and mutability of the gene. Additionally, a sixth individual with a de novo mutation in PPP3CA was connected to this study through GeneMatcher. Based on these findings, we securely implicate PPP3CA in early-onset refractory epilepsy and further support the emerging role for synaptic dysregulation in epilepsy.

The Epilepsy Genetics Initiative: Systematic reanalysis of diagnostic exomes increases yield

“…This novel exon was not included in the consensus coding sequence (CCDS) and was not routinely interrogated by clinical laboratories . The PPP3CA diagnoses were possible due to new observations based on EGI and collaborator data, and EGI Case 3 was included in a paper to implicate variants in the gene as causative for epilepsy . Many of the additional diagnoses were not possible at the time of clinical sequencing, as the respective genes were not implicated with disease until after the initial diagnostic WES.…”

“…PPP3CA was one of the first genes in which a candidate variant was identified in the EGI cohort. This resulted in a collaborative publication describing the association of PPP3CA with severe neurodevelopmental disease with seizures and allowed for a new diagnosis for two EGI families (Cases 3 and 4). Combining exome sequence data from many different studies or databases has historically been extremely valuable in facilitating the discovery of novel genes, like it was for PPP3CA, and will likely continue to be in the short term.…”

“…11 In two cases, we reported on a variant in PPP3CA, an epilepsy gene newly described through a collaborative effort that involved EGI. 12 Additional diagnoses include one case each with a variant identified in the FGF12, HNRNPU, SATB2, or STAG2 genes. See Table 1 for additional details.…”

“…11 The PPP3CA diagnoses were possible due to new observations based on EGI and collaborator data, and EGI Case 3 was included in a paper to implicate variants in the gene as causative for epilepsy. 12 Many of the additional diagnoses were not possible at the time of clinical sequencing, as the respective genes were not implicated with disease until after the initial diagnostic WES. For example, in EGI Case 1 (see Table 1), the subject's clinical WES in 2014 yielded several variants of seven individuals with epileptic encephalopathy and was functionally characterized to disrupt the gene via a gain-offunction mechanism.…”

“…Randall Stewart, 5 Vicky Whittemore. 5 EGI Enrollment Group: Kaitlin Angione, 6 Carl W. Bazil, 7 Louise Bier, 2 Judith Bluvstein, 8 Elise Brimble, 9 Colleen Campbell, 10 Gianpiero Cavalleri, 11,12 Chelsea Chambers, 13 Hyunmi Choi, 7 Maria Roberta Cilio, 4,14 Michael Ciliberto, 15 Susannah Cornes, 4 Norman Delanty, 11,12 Scott Demarest, 6 Orrin Devinsky, 8 Dennis Dlugos, 16 Holly Dubbs, 16 Patricia Dugan, 8 Michelle E. Ernst, 2 Melissa Gibbons, 6 Howard P. Goodkin, 13 Ingo Helbig, 16 Laura Jansen, 13 Kaleas Johnson, 4 Charuta Joshi, 6 Natalie C. Lippa, 2 Eric Marsh, 16,17 Alejandro Martinez, 16 John Millichap, 18,19 Maureen S. Mulhern, 2 Adam Numis, 4,14 Kristen Park, 6 Tommaso Pippucci, 20 Annapurna Poduri, 21 Brenda Porter, 9 Brigid Regan, 1 Tristan T. Sands, 2,22 Ingrid E. Scheffer, 1,23,24 John M. Schreiber, 25 Beth Sheidley,…”