Conradi-Hunermann syndrome (CDPX2) is X-linked dominant disorder appeared with aberrant punctuate calcification. The skeletal cells derived from the marrow stroma are active in maintaining the skeletal formation. We obtained mesenchymal stem cells from a patient with CDPX2 and studied the formation of colony forming unit-fibroblast (CFU-F) in vitro in comparison cells obtained from normal donors. Cultured cells were studied morphologically and subjected to gene expression analysis. Marrow stromal cells (MSC)-chondrodysplasia punctuate (CDP) cells from CDPX2 were identified by their mosaic morphology formed three phenotypically distinct types of CFU-F colonies. One type consisted of normal fibroblasts with developed cell body and cellular processes; the second type contained pathological small cells without processes; and the third type comprised of mixed cells. We compared gene expression by the MSC-CDP to cells from normal donors. Transcription factors analyzed proliferation potential were similar in both normal and mixed colonies of MSC-CDP and similar to normal MSCs. The message expression for cytokines and extra cellular matrix (ECM) proteins revealed similar expression for biglycan, osteocalcin, and osteonectin, while IL-6, IL-11, and M-CSF mRNA levels were significantly higher in normal cells than in MSC-CDP. Mixed cells had elevated levels for IL-6 and M-CSF mRNA, but expressed IL-11 at the normal range. The studied genes were expressed at lower levels by the pathological (MSC-CDP) cells compared to normal ones. Hence, MSC-CDP was demonstrated to display abnormal morphology and transcription of several investigated genes. This study further illuminates the basis of the mosaic pattern of mesenchymal cells derived from a patient affected with CDPX2, and their gene expression involvement.