Nonselective ligand-gated cation channel probably playing a role in the regulation of membrane trafficking events. Acts as Ca(2+)-permeable cation channel with inwardly rectifying activity (PubMed:17989217). Mediates release of Ca(2+) from endosomes to the cytoplasm, contributes to endosomal acidification and is involved in the regulation of membrane trafficking and fusion in the endosomal pathway (By similarity). Does not seem to act as mechanosensory transduction channel in inner ear sensory hair cells. Proposed to play a critical role at the cochlear stereocilia ankle-link region during hair-bundle growth (PubMed:18801844). Involved in the regulation of autophagy. Through association with GABARAPL2 may be involved in autophagosome formation possibly providing Ca(2+) for the fusion process (PubMed:24269818). Through a possible and probably tissue-specific heteromerization with MCOLN1 may be at least in part involved in many lysosome-dependent cellular events. Possible heteromeric ion channel assemblies with TRPV5 show pharmacological similarity with TRPML3 (By similarity). Inhibited by lumenal H(+) and Na(+). The channel pore shows dynamic behavior and undergoes spontaneous, Ca(2+)-dependent modulation when conducting Ca(2+). Homotetramer. Can heterooligomerize with MCOLN1; heteromeric assemblies have different channel properties as compared to the respective homooligomers and may be tissue-specific. May heterooligomerize with TRPV5 to form a functional distinct ion channel (By similarity). Interacts with GABARAPL2 (PubMed:24269818). Recycles between the plasma membrane and intracellular compartments by a dynamin-dependent endocytic pathway (By similarity). In the cochlea located at the base of stereocilia near the position of the ankle links. Expressed in the cochlea; particularly in the inner and outer hair cells (at protein level). The most N-terminal extracellular/lumenal domain (referred to as I-II linker or polycystin-mucolipin domain) contributes to a structure with a four-fold rotational symmetry in a tetrameric assembly; the structure contains a central highly electronegative pore with a 14 A diameter. The pore is critical for Ca(2+) and pH regulation. The protruding structure formed by the I-II linkers may contain all the interaction sites with lipids and proteins in the endolysosomal lumen. N-glycosylated. Defects in Mcoln3 are the cause of the varitin-waddler (Va) phenotype. Classical Va mice exhibit early-onset hearing loss, vestibular defects, pigmentation abnormalities and perinatal lethality. The phenotype varitin-waddler Jackcon (Va-J), which arose in a cross segregating for Va, is similar but less severe. No severe auditory and vestibular phenotype; does not lead to circling behavior, balance impairment or hearing loss. Belongs to the transient receptor (TC 1.A.4) family. Polycystin subfamily. MCOLN3 sub-subfamily.