The presence of the triad of HDR and enamel hypomineralization may be caused by the frameshift variants in GATA3; the atypical hypercalciuria occurring both in the patient and his father may be explained by the heterozygous missense variant in SLC34A3. Furthermore, this report reaffirmed the importance of the trio whole‐exome sequencing and consideration of other genetic causes for patients with complex clinical phenotypes. Here, SLC34A3 is linked to Hypercalciuria.