Mutations in the PP2A regulatory subunit B family genes PPP2R5B, PPP2R5C and PPP2R5D cause human overgrowth

Abstract

Overgrowth syndromes comprise a group of heterogeneous disorders characterised by excessive growth parameters, often in association with intellectual disability. To identify new causes of human overgrowth, we have been undertaking trio-based exome sequencing studies in overgrowth patients and their unaffected parents. Prioritisation of functionally relevant genes with multiple unique de novo mutations revealed four mutations in protein phosphatase 2A (PP2A) regulatory subunit B family genes protein phosphatase 2, regulatory Subunit B', beta (PPP2R5B); protein phosphatase 2, regulatory Subunit B', gamma (PPP2R5C); and protein phosphatase 2, regulatory Subunit B', delta (PPP2R5D). This observation in 3 related genes in 111 individuals with a similar phenotype is greatly in excess of the expected number, as determined from gene-specific de novo mutation rates (P = 1.43 × 10(-10)). Analysis of exome-sequencing data from a follow-up series of overgrowth probands identified a further pathogenic mutation, bringing the total number of affected individuals to 5. Heterozygotes shared similar phenotypic features including increased height, increased head circumference and intellectual disability. The mutations clustered within a region of nine amino acid residues in the aligned protein sequences (P = 1.6 × 10(-5)). We mapped the mutations onto the crystal structure of the PP2A holoenzyme complex to predict their molecular and functional consequences. These studies suggest that the mutations may affect substrate binding, thus perturbing the ability of PP2A to dephosphorylate particular protein substrates. PP2A is a major negative regulator of v-akt murine thymoma viral oncogene homolog 1 (AKT). Thus, our data further expand the list of genes encoding components of the phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K)/AKT signalling cascade that are disrupted in human overgrowth conditions.

Figure 1.

PP2A-B56 mutations in human overgrowth. (A) Protein schematic showing the distribution of PP2A-B56 subunit mutations in individuals with overgrowth (above, red lollipops) versus variants identified in the ICR1000 control series (below, grey lollipops). The shared core B56 domain is shown in orange and the intra-repeat loop 2 region in blue. (B) PP2A-B56 subunit mutations mapped onto the PP2A-B56γ complex. PP2A-B56γ is shown in orange, the catalytic subunit is in light brown and the scaffold subunit is in yellow. The intra-repeat loop 2 of PP2A-B56γ is highlighted in blue. The residues corresponding to the mutations identified are shown as red spheres. Inset: interaction of PP2A-B56γ p.Glu153 with the PP2A-Cα subunit. The glutamate side chain forms an ion pair interaction and water-mediated H-bonds to Arg residues from the catalytic subunit. (C) Facial characteristics of individuals with PP2A-B56 subunit mutations. Growth parameters and clinical features are described in Table 1. Specific consent to publish facial photographs was obtained for all individuals.