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In this review, we examine the clinical features and differential diagnoses of this group of syndromes, including autosomal recessive polycystic kidney disease (ARPKD), juvenile nephronophthisis (NPHP), Meckel-Gruber syndrome (MKS), Bardet-Biedl syndrome (BBS), and Jeune asphyxiating thoracic dystrophy (JATD). Extrahepatic manifestations include mostly bone and central nervous system abnormalities, dysmorphic features, and developmental delay. Previously, it has been suggested that ARPKD, JATD, and Ellis-van Creveld syndrome (EvC) may arise from defects in differentiation in a common developmental pathway. 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