Proposed to be involved in endosomal maturation implicating in part VPS33B. In epithelial cells, the VPS33B:VIPAS39 complex may play a role in the apical RAB11A-dependent recycling pathway and in the maintenance of the apical-basolateral polarity (PubMed:20190753). May play a role in lysosomal trafficking, probably via association with the core HOPS complex in a discrete population of endosomes; the functions seems to be independent of VPS33B (By similarity). May play a role in vesicular trafficking during spermatogenesis (By similarity). May be involved in direct or indirect transcriptional regulation of E-cadherin. Interacts with VPS33B. Associates with the homotypic fusion and vacuole protein sorting (HOPS) complex; impaired by VPS33B (By similarity). Interacts with RAB11A (PubMed:20190753). Colocalizes in clusters with VPS33B at cytoplasmic organelles. Vipar-deficient inner medullary collecting duct cells display abnormal expression of membrane proteins such as Ceacam5, structural and functional tight junction defects and reduced E-cadherin expression. Belongs to the SPE39 family.