Involved in early stages of melanosome biogenesis and maturation. Component of the biogenesis of lysosome-related organelles complex-2 (or BLOC2) composed of HPS3, HPS5 and HPS6. Interacts with HPS5 and HPS6. Found in heart, brain, spleen, liver, lung, kidney and testis. Defects in Hps3 are the cause of the cocoa (coa) mutant, which is characterized by hypopigmentation and platelet dysfunction (PubMed:11707070).