We report a male patient with three copy-number variations (CNVs) and unique phenotype. He carried ~11.2 Mb terminal duplication on 4q, ~13.4 Mb terminal deletion on 7q and ~1.7 Mb interstitial duplication on Xp22.31, which were identified by array-based comparative genomic hybridization. He manifested mental retardation, mild brain anomalies and skeletal deformities ascribable to these CNVs, together with central precocious puberty and mild adrenocorticotropic hormone overproduction of unknown etiologies.