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A rare mutant of OFD1 gene responsible for Joubert syndrome with significant phenotype variation

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Abstract

Joubert syndrome (JBTS), a rare genetic disorder resulted from primary cilium defects or basal-body dysfunction, is characterized by agenesis of cerebellar vermis and abnormal brain stem. Both genotypes and phenotypes of JBTS are highly heterogeneous. The identification of pathogenic gene variation is essential for making a definite diagnosis on JBTS. Here, we found that hypoplasia of cerebellar vermis occurred in three male members in a Chinese family. Then, we performed whole exome sequencing to identify a novel missense mutation c.599T > C (p. L200P) in the OFD1 gene which is the candidate gene of X-linked JBTS (JBST10). The following analysis showed that the variant was absent in the 1000 Genomes, ExAC and the 200 female controls; the position 200 Leucine residue was highly conserved across species; the missense variant was predicted to be deleterious using PolyPhen-2, PROVEAN, SIFT and Mutation Taster. The OFD1 expression was heavily lower in the proband and an induced male fetus compared with a healthy male with a wild-type OFD1 gene. The in vitro expression analysis of transiently transfecting c.599T or c.599C plasmids into HEK-293T cells confirmed that the missense mutation caused OFD1 reduction at the protein level. And further the mutated OFD1 decreased the level of Gli1 protein, a read-out of Sonic hedgehog (SHH) signaling essential for development of central neural system. A known pathogenic variant c.515T > C (p. L172P) showed the similar results. All of these observations suggested that the missense mutation causes the loss function of OFD1, resulting in SHH signaling impairs and brain development abnormality. In addition, the three patients have Dandy-Walker malformation, macrogyria and tetralogy of Fallot, respectively, the latter two of which are firstly found in JBTS10 patients. In conclusion, our findings expand the context of genotype and phenotype in the JBTS10 patients.

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Data availability

The raw WES data is deposited in BioProject database and the accession codes: PRJNA660941.

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Acknowledgements

The authors would like to thank the professor Yang Xiaoyan of West China Second University Hospital for her contribution to this article.

Funding

This study was funded by National Natural Science Foundation of China with Grant (No. 81871203).

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Authors and Affiliations

Authors

Contributions

YWZ, YQL and YY designed the study. YWZ investigated the subject and drafted this manuscript. HBQ analyzed image data. NL provided control samples. XYL was responsible for statistical analysis. YY revised the manuscript.

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Correspondence to Yuan Yang.

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The authors declare that they have no conflict of interest.

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This study was approved by the ethic committee of West China hospital and the Second Clinical Institute of North Sichuan Medical College.

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All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

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Communicated by Stefan Hohmann.

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Zhang, Yw., Qu, Hb., Long, N. et al. A rare mutant of OFD1 gene responsible for Joubert syndrome with significant phenotype variation. Mol Genet Genomics 296, 33–40 (2021). https://doi.org/10.1007/s00438-020-01726-1

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