We note that we observe a strong association of a missense variant in the APRT gene encoding adenine phosphoribosyltransferase (rs104894506[A], NP_000476.1:p.Asp65Val, MAF=1.26%) with kidney stones under the recessive model (OR=31.97, P=6.83 × 10−10). Here, APRT is linked to nephrolithiasis.