We looked for evidence of altered gene expression in Alx3-deficient embryos from diabetic pregnancies showing no major malformations to avoid the detection of changes that could be attributable to alterations in cellular composition associated to dysmorphogenesis. This is important because incomplete penetrance of congenital malformations constitutes a common feature of birth defects induced by maternal diabetes, so that a proportion of embryos develop normally despite the detection of significant changes in gene expression16, 63. This may be due to increased variability in gene expression levels induced by maternal diabetes, so that defects would only appear when expression of certain genes fall below a given threshold63. In this context, Alx3 deficiency would render the embryos prone to the appearance of overt developmental alterations by increasing permissively the magnitude of these changes. Therefore, changes in the expression of genes observed in Alx3-deficient embryos from diabetic mothers do not necessarily identify direct targets of regulation by ALX3. Instead, these changes reflect a role for ALX3 as a protective genetic buffer to temper the effects of hyperglycaemia on gene expression levels during a critical period of development.