PARD3 gene variation as candidate cause of nonsyndromic cleft palate only

Nonsyndromic cleft palate only (NSCP) is a common congenital malformation worldwide. In this study, we report a three-generation pedigree with NSCP following the autosomal-dominant pattern. Whole-exome sequencing and Sanger sequencing revealed that only the frameshift variant c.1012dupG [p. E338Gfs*26] in PARD3 cosegregated with the disease. In zebrafish embryos, ethmoid plate patterning defects were observed with PARD3 ortholog disruption or expression of patient-derived N-terminal truncating PARD3 (c.1012dupG), which implicated PARD3 in ethmoid plate morphogenesis. PARD3 plays vital roles in determining cellular polarity. Compared with the apical distribution of wild-type PARD3, PARD3-p. E338Gfs*26 mainly localized to the basal membrane in 3D-cultured MCF-10A epithelial cells. The interaction between PARD3-p. E338Gfs*26 and endogenous PARD3 was identified by LC-MS/MS and validated by co-IP. Immunofluorescence analysis showed that PARD3-p. E338Gfs*26 substantially altered the localization of endogenous PARD3 to the basement membrane in 3D-cultured MCF-10A cells. Furthermore, seven variants, including one nonsense variant and six missense variants, were identified in the coding region of PARD3 in sporadic cases with NSCP. Subsequent analysis showed that PARD3-p. R133*, like the insertion variant of c.1012dupG, also changed the localization of endogenous full-length PARD3 and that its expression induced abnormal ethmoid plate morphogenesis in zebrafish. Based on these data, we reveal PARD3 gene variation as a novel candidate cause of nonsyndromic cleft palate only.