Critical genes like <i>FOXG1</i>, <i>NKX2</i>-1, <i>PAX9</i> were identified.<h4>Case presentation</h4>We performed whole exome sequencing (WES) and copy number variation sequencing (CNV-seq) for a patient with mild speech and motor developmental delay, short stature, recurrent pulmonary infections, tooth agenesis and triad of brain-lung-thyroid syndrome. This evidence concerns the gene PAX9 and brain-lung-thyroid syndrome.