Two heterozygous missense changes in the SOX3 and GLI2 genes, associated with holoprosencephaly, were found in KS patients—the first previously unreported in any subject without a mutation in other examined known KS/IHH genes, and the second in patients with a deleterious variant in PROKR2: p.R85H (c.254G>A, Figure 1). Here, SOX3 is linked to holoprosencephaly.