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Significance We identify AP-3–mediated targeting of flippase ATP8A1 to lamellar bodies, lysosome-related organelles that store pulmonary surfactant for secretion from alveolar epithelial cells. Genetic AP-3 loss in cultured alveolar epithelial cells and in thepearl mouse model causes ATP8A1 retention in early sorting and/or recycling endosomes and concomitant accumulation of phosphatidylserine on endosomal membranes. This in turn elicits a toxic gain-of-function through Yes-activating protein and initiates lung injury programs that may contribute to progressive lung fibrosis associated with Hermansky Pudlak syndrome type 2.

AP-3–dependent targeting of flippase ATP8A1 to lamellar bodies suppresses activation of YAP in alveolar epithelial type 2 cells