<p>Mutations in PARK7, which encodes DJ-1, cause autosomal recessive early-onset Parkinson’s disease. DJ-1 contributes to mitochondrial homeostasis and ER-mitochondria communication, but how the pathogenic L166P and M26I variants affect BNIP3/BNIP3L-associated phenotypes remains incompletely understood. Here, we examined DJ-1 variant-dependent changes in BNIP3/BNIP3L interactions, mitochondrial morphology, ER-mitochondria proximity-associated readouts, and global intracellular Ca²⁺ responses in PC-12 and SH-SY5Y cell models. AlphaFold3-based interface prediction, co-immunoprecipitation, and GST pull-down assays supported interactions involving DJ-1, BNIP3, and BNIP3L, including binding to selected BNIP3- and BNIP3L-derived peptide regions. DJ-1 WT and M26I showed detectable binding to BNIP3-derived regions, whereas the unstable L166P variant showed reduced BNIP3 binding even after partial restoration of L166P abundance with MG132. Reciprocal co-immunoprecipitation and knockdown experiments further supported an association between BNIP3 and BNIP3L in these cells. In L166P expressing cells with GRP75 knockdown, BNIP3 depletion increased the ER-mitochondria distance and reduced the length of the ER-mitochondria proximity region. Colocalization analyses showed DJ-1 variant-dependent changes in proximity-associated imaging readouts, while immunoblotting identified reduced VDAC1 and MFN1 levels after BNIP3 depletion in mutant expressing cells. BNIP3 depletion reduced the relative 2-APB evoked Fluo-4 response in WT, L166P and M26I expressing cells by 40.7%, 76.7%, and 42.5%, respectively. Overall, these findings may reflect altered DJ-1/BNIP3/BNIP3L interaction profiles and BNIP3 sensitive changes in ER-mitochondria proximity associated and global intracellular Ca²⁺ readouts, particularly in L166P-expressing cells, although direct validation is still required.</p>