Osteogenesis imperfecta (OI) is a heritable and chronically debilitating skeletal dysplasia. Patients with OI typically present with reduced bone mass, tendency for recurrent fractures, short stature and bowing deformities of the long bones. Mutations causative of OI have been identified in over 20 genes involved in collagen folding, posttranslational modification and processing, and in bone mineralization and osteoblast development. In 2016, we described the first X-linked recessive form of OI caused byMBTPS2missense variants in patients with moderate to severe phenotypes.MBTPS2encodes site-2 protease, a Golgi transmembrane protein that activates membrane-tethered transcription factors. These transcription factors regulate genes involved in lipid metabolism, bone and cartilage development, and ER stress response. The interpretation of genetic variants inMBTPS2is complicated by the gene’s pleiotropic properties;MBTPS2variants can also cause the dermatological conditions Ichthyosis Follicularis, Atrichia and Photophobia (IFAP), Keratosis Follicularis Spinulosa Decalvans (KFSD) and Olmsted syndrome (OS) without skeletal abnormalities typical of OI. Using control and patient-derived fibroblasts, we previously identified gene expression signatures that distinguishMBTPS2-OI fromMBTPS2-IFAP/KFSD and observed stronger suppression of genes involved in fatty acid metabolism inMBTPS2-OI than inMBTPS2-IFAP/KFSD; this was coupled with alterations in the relative abundance of fatty acids inMBTPS2-OI. Furthermore, we observed a reduction in collagen deposition in the extracellular matrix byMBTPS2-OI fibroblasts. Here, we extrapolate our observations in the molecular signature unique toMBTPS2-OI to infer the pathogenicity of a novelMBTPS2c.516A>C (p.Glu172Asp) variant of unknown significance in a male proband. The pregnancy was terminated at gestational week 21 after ultrasound scans showed bowing of femurs and tibiae and shortening of long bones particularly of the lower extremity; these were further confirmed by autopsy. By performing transcriptional analyses, gas chromatography-tandem mass spectrometry-based quantification of fatty acids and immunocytochemistry on fibroblasts derived from the umbilical cord of the proband, we observed perturbations in fatty acid metabolism and collagen production similar to what we previously described inMBTPS2-OI. These findings support pathogenicity of theMBTPS2variant p.Glu172Asp as OI-causative and highlights the value of extrapolating molecular signatures identified in multiomics studies to characterize novel genetic variants.