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Background  Joubert syndrome (OMIM 213300) is an autosomal recessive disorder with gene heterogeneity. Causal genes and their variants have been identified by sequencing or other technologies for Joubert syndrome subtypes.    Case presentation  A two-year-old boy was diagnosed with Joubert syndrome by global development delay and molar tooth sign of mid-brain. Whole exome sequencing was performed to detect the causative gene variants in this individual, and the candidate pathogenic variants were verified by Sanger sequencing. We identified two pathogenic variants (NM_006346.2: c.1147delC and c.1054A > G) of  PIBF1  in this Joubert syndrome individual, which is consistent with the mode of autosomal recessive inheritance.    Conclusion  In this study, we identified two novel pathogenic variants in  PIBF1  in a Joubert syndrome individual using whole exome sequencing, thereby expanding the  PIBF1  pathogenic variant spectrum of Joubert syndrome.

Identification of two novel pathogenic variants of PIBF1 by whole exome sequencing in a 2-year-old boy with Joubert syndrome