A 223-kb de novo deletion of PAX9 in a patient with oligodontia.

The PAX (paired box) genes are a family of transcription factors critical for fetal growth and organogenesis. Abnormalities of PAX2, PAX3, PAX6, and PAX9 are associated with various congenital craniofacial anomalies, including tooth abnormalities. We present here a boy with oligodontia and language delay. Dental x-rays showed that he lacked primary molars and was missing most of his permanent teeth. A genome-wide, single-nucleotide polymorphism-based microarray revealed a de novo 223-kb heterozygous deletion on 14q13.3 that included the PAX9 gene. In addition, the array showed 2 copies of the X chromosome and 1 copy of the Y chromosome, diagnostic for Klinefelter syndrome. The findings in this patient illustrate the role of the PAX9 gene in tooth development and provide the first example of a de novo deletion of 14q13.3 manifesting primarily with oligodontia. This report also supports the utility of genome-wide microarrays in determining the genetic cause of craniofacial abnormalities.