Progressive pseudorheumatoid dysplasia (PPD) is a rare autosomal recessive cartilage disorder caused by biallelic variants in CCN6, which encodes the matricellular protein WISP3. Although WISP3 is thought to contribute to extracellular matrix (ECM) homeostasis, its precise molecular role in PPD remains unclear. To elucidate how disease-associated CCN6 variants affect chondrocyte function, we overexpressed four variants—p.Cys52*, p.Tyr109*, p.Gly83Glu, and p.Cys114Trp—all located within the IGFBP domain, and evaluated their impact on parameters including redox balance, ER stress, ECM remodeling, gene expression, and protein–protein interactions. The p.Cys52* variant resulted in rapid degradation of WISP3, indicating a complete loss-of-function. The p.Tyr109* variant disrupted ECM regulation, markedly reducing protein interaction capacity, which was correlated with elevated mitochondrial ROS (mtROS) levels and triggered a strong response that led to programmed cell death. Although both missense variants yielded full-length proteins, their effects diverged significantly: p.Gly83Glu induced minor cellular alterations, whereas p.Cys114Trp caused severe protein destabilization, increased ROS accumulation, and high levels of ER stress. Proteomic analysis revealed that p.Cys114Trp acquired novel interaction partners, suggesting a potential gain-of-function mechanism. Collectively, these findings demonstrate that the functional consequences of CCN6 variants depend not only on variant type or domain location but also on their positional and structural context. The distinct cellular responses elicited by each variant underscore the importance of functional validation in modeling PPD pathogenesis and offer valuable biological and therapeutic perspectives.