Regulator of TGF-beta/activin signaling, inhibiting SMAD3- and activating SMAD2-dependent transcription. Acts by interfering with SMAD3/SMAD4 complex formation, this would lead to inhibition of SMAD3-dependent transcription and relieve SMAD3 inhibition of SMAD2-dependent promoters, thus increasing SMAD2- dependent transcription. Does not affect TGF-beta-induced SMAD2 or SMAD3 phosphorylation, nor SMAD2/SMAD4 complex formation. . Plays a role in vesicle-mediated protein trafficking to lysosomal compartments including the endocytic membrane transport and autophagic pathways. Acts as a component of the HOPS endosomal tethering complex. This complex is proposed to be involved in the Rab5- to-Rab7 endosome conversion probably implicating MON1A/B, and via binding SNAREs and SNARE complexes to mediate tethering and docking events during SNARE-mediated membrane fusion. The HOPS complex is proposed to be recruited to Rab7 on the late endosomal membrane and to regulate late endocytic, phagocytic and autophagic traffic towards lysosomes (PubMed:23351085). Involved in homotypic vesicle fusions between late endosomes and in heterotypic fusions between late endosomes and lysosomes (PubMed:11448994, PubMed:23167963, PubMed:23351085). Required for fusion of endosomes and autophagosomes with lysosomes (PubMed:25783203, PubMed:37821429). {ECO:0000269|PubMed:11448994, ECO:0000269|PubMed:23167963, ECO:0000269|PubMed:25783203, ECO:0000269|PubMed:33422265, ECO:0000269|PubMed:37821429, ECO:0000305|PubMed:23351085}. This is the function of Ensembl gene identifier ENSG00000166887 (VPS39, VPS39 subunit of HOPS complex).