We describe a chromosome rearrangement, ins(7;13)(q32q34;q32), which segregates in a three generation family, giving rise to three individuals with an unbalanced rearrangement. Two of the individuals, a sister and a brother, were investigated further in this study. They had minor facial dysmorphism and neuropsychiatric disorders including mental retardation, language delay and epilepsy. The sister had primary amenorrhea. Array CGH revealed a 12.2 Mb deletion at 7q34–q36.2 including more than 60 genes where CNTNAP2 and NOBOX are of special interest. Comparison of the clinical and cytogenetic findings of our patients with previously reported patients, supports that haploinsuffiency of CNTNAP2 can result in language delay and/or autism spectrum disorder. Furthermore, we report on the second women with a deletion involving NOBOX who is affected by primary amenorrhea. © 2010 Wiley-Liss, Inc.