Lead SNP rs72823645 (SLC35B3, 6p24.3) was associated with both non-syndromic cleft palate only (nsCPO) and Pierre Robin sequence (PRS) (albeit not genome wide significant in PRS, P = 2.82 × 10−5), as well as being nominally associated with cleft lip phenotypes with attenuated effects in the same direction. Here, SLC35B3 is linked to cleft palate.