Functional analysis of a novel de novo variant in PPP5C associated with microcephaly, seizures, and developmental delay

• Published in: Molecular genetics and metabolism 2022-05, Vol.136 (1), p.65-73
• Main Authors: Fielder, Sara M., Rosenfeld, Jill A., Burrage, Lindsay C., Emrick, Lisa, Lalani, Seema, Attali, Ruben, Bembenek, Joshua N., Hoang, Hieu, Baldridge, Dustin, Silverman, Gary A., Schedl, Tim, Pak, Stephen C.
• Format: Article
• Language: English
• Subjects: Animals; C. elegans; Caenorhabditis elegans - genetics; Caenorhabditis elegans Proteins - genetics; Child; Developmental delay; Developmental Disabilities - genetics; F-Box Proteins - genetics; Humans; Microcephaly; Microcephaly - genetics; Mutation, Missense; Nuclear Proteins - genetics; Phenotype; Phosphoprotein Phosphatases - genetics; PPH-5; PPP5C; Seizures - genetics; Separase - genetics
• ISSN: 1096-7192; 1096-7206
• DOI: 10.1016/j.ymgme.2022.03.007

We describe a proband evaluated through the Undiagnosed Diseases Network (UDN) who presented with microcephaly, developmental delay, and refractory epilepsy with a de novo p.Ala47Thr missense variant in the protein phosphatase gene, PPP5C. This gene has not previously been associated with a Mendelian disease, and based on the population database, gnomAD, the gene has a low tolerance for loss-of-function variants (pLI = 1, o/e = 0.07). We functionally evaluated the PPP5C variant in C. elegans by knocking the variant into the orthologous gene, pph-5, at the corresponding residue, Ala48Thr. We employed assays in three different biological processes where pph-5 was known to function through opposing the activity of genes, mec-15 and sep-1. We demonstrated that, in contrast to control animals, the pph-5 Ala48Thr variant suppresses the neurite growth phenotype and the GABA signaling defects of mec-15 mutants, and the embryonic lethality of sep-1 mutants. The Ala48Thr variant did not display dominance and behaved similarly to the reference pph-5 null, indicating that the variant is likely a strong hypomorph or complete loss-of-function. We conclude that pph-5 Ala48Thr is damaging in C. elegans. By extension in the proband, PPP5C p.Ala47Thr is likely damaging, the de novo dominant presentation is consistent with haplo-insufficiency, and the PPP5C variant is likely responsible for one or more of the proband's phenotypes.