Emerging evidence implicates ER stress caused by unfolded mutant proteins in chondrocytes as the underlying pathology of chondrodysplasias. ER stress is triggered in hypertrophic chondrocytes (HCs) in a mouse model (13del) of metaphyseal chondrodysplasia type Schmid (MCDS) caused by misfolded mutant collagen X proteins, but the HCs do not undergo apoptosis, rather chondrocyte differentiation is altered causing skeletal abnormality. How 13del HCs can escape from apoptosis and survive ER stress is not understood. We compared using label-free quantitative mass spectrometry approach the proteomes of HCs isolated from 13del growth plates with normal HCs. In this paper we reveal significant changes in levels of proteins involved in in actin remodeling, glycolysis and ER-mitochondria communication in 13del HCs chondrocytes. Previous in vitro studies of chronic ER stress showed down-regulation of glycolysis and disrupted mitochondrial function leading to cell death. Our data showed that glucose uptake was maintained in ATDC5 chondrocytic cell lines expressing 13del collagen X. Furthermore expression of mitochondrial calcium channels was reduced while mitochondrial membrane polarity was maintained in in vivo 13del chondrocytes. Thus we propose that 13del HCs survive by a mechanism whereby changes in ER-mitochondria communication reduce import of calcium coupled with maintenance of mitochondrial membrane polarity.