We report causal and likely causal variants (whereof eight novel) in the following genes (Table 1): 1) CS core genes FGFR2, TWIST1, and TCF12; 2) HDAC9, a gene situated in a candidate region with regulatory elements for TWIST1; 3) genes occasionally associated with CS (e.g., FOXP1, NSD2, and YY1); and 4) KIAA0586, which was not previously associated with CS. This evidence concerns the gene HDAC9 and Cowden syndrome 1.