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Joubert syndrome (JS) is a ciliopathy that is defined primarily by typical cerebellar structural and ocular motility defects. The genetic heterogeneity of this condition is significant with 16 genes identified to date. We have used a combination of autozygome-guided candidate gene mutation analysis and exome sequencing to identify the causative mutation in a series of 12 families. The autozygome approach identified mutations inRPGRIP1L,AHI1,TMEM237, andCEP290, while exome sequencing revealed families with truncating mutations inTCTN1andC5ORF42. Our study, the largest comprehensive molecular series on JS, provides independent confirmation of the recently reportedTCTN1,TMEM237, andC5ORF42as bona fide JS disease genes, and expands the allelic heterogeneity of this disease.