In this report, we present the case of a Saudi baby boy with a rare de novo interstitial deletion of chromosome 2q14.1-q22.1. His karyotype was confirmed as 46,XY 1(?)q14.2-1q21.3) but further investigation using chromosomal microarray analysis yielded the deletion breakpoints as 2q14.1q22.1. To date, only 10 cases have been reported within or spanning the deletion of the 2q13-2q22.1 region. In comparison to the established cases, our proband shares similar features, such as bitemporal narrowing, deep vein thrombosis, and horseshoe kidney. However, our proband presented with new features which included congenital knee dislocation, congenital vertical talus, bilateral hip dislocation, and myelomeningocele. Moreover, all the reported cases share GLI2 deletion which may reflect the phenotypic features in patients with the deletion of 2q14.1q22.1.