VPS36 is a subunit of the endosomal sorting complex required for transport II (ESCRT-II). This complex is required for multivesicular body (MVB) formation and for sorting endosomal cargo proteins into MVBs. The MVB pathway delivers transmembrane proteins into the lumen of the lysosome, where they are degraded. ESCRT-II is probably involved in recruiting the ESCRT-III complex. The VPS36 protein can bind ubiquitin, which probably contributes to the endosomal sorting of ubiquitinated cargo by ESCRT complexes. It also binds phosphoinositides such as PtdIns(3,4,5)P3.

The VPS36 gene encodes a protein of the VPS36 family, and HGNC places it in the ESCRT-II gene group. UniProt records its subcellular locations as the cytoplasm, endosome, late endosome, membrane and nucleus. The mouse and rat orthologs are both named Vps36, which is useful when planning work across model systems.

Beyond endocytic sorting, the ESCRT-II complex may play a role in transcription regulation, possibly through its interaction with ELL. NCBI Gene notes that a similar complex in rat is associated with RNA polymerase elongation factor II. The name Eap45 reflects this association. The gene was previously called C13orf9 (chromosome 13 open reading frame 9), and earlier HGNC names referred to the yeast homolog. Researchers studying the VPS36 gene or protein usually do so in the context of endosomal trafficking, ubiquitin-dependent sorting and ESCRT assembly.