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. 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. 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. High levels detected in liver and small intestine of larvae at 5 days post-fertilization. Belongs to the SPE39 family.