Genetic characteristics of 51 retinitis pigmentosa families

Objective  To analyze the disease-causing genes of families affected by retinitis pigmentosa (RP).

Methods  A pedigree investigation study was performed.The clinical data of 51 Chinese families with RP treated at the Renmin Hospital of Wuhan University from June 2019 to December 2022 were collected, including patient history, family history and clinical data of ophthalmic examination.Ophthalmic examination including best corrected visual acuity, slit lamp microscopy, color fundus photography, fundus autofluorescence, macular optical coherence tomography, visual field and electroretinogram.Peripheral blood samples from patients and their family members were collected for DNA extraction and whole exome sequencing.The mutation sites found were analyzed by bioinformatics and verified by Sanger sequencing.The pathogenicity of the missense mutations was predicted using SIFT, Polyphen and other online software.Conservation of the missense mutation site was evaluated using Mutation Taster.The shear mutation was predicted using varSEAK and spliceAI.The amino acid sequences of the newly discovered mutation sites were compared using Clustalw software.This study adhered to the Declaration of Helsinki.The study protocol was approved by the Ethics Committee of Renmin Hospital of Wuhan University (No.WDRY2019-K032).

Results  Among the 51 families, two proband patients had hearing impairment and were diagnosed as Usher syndrome.In addition to typical RP features, the two proband patients also showed yellow-white crystalline substance deposits in fundus imaging, while the other proband patients showed typical RP.A total of 38 single nucleotide variants (SNVs) and 3 copy number variants were detected in 15 pathogenic genes in 29 of 51 families, including PRPF6, PRPF31, RHO, CYP4V2, USH2A, EYS, MERTK, PCDH15, ABCA4, BBS2, PROM1, SPATA7, RPE65, RPGR and OFD1 genes.There were 6 of the 38 SNVs that were novel variants that had not been reported, which were USH2A gene c.12523T>C(p.Trp4175Arg), c.1723T>C(p.Cys575Arg), c.1875C>G(p.Phe625Leu), CYP4V2 gene c.1441C>T(p.Leu481Phe), MERTK gene c.2487-8A>G and PCDH15 gene c. 5183del(p.Arg1728LysfsTer116).SIFT and Polyphen prediction software predicted that amino acid changes caused by the 4 missense variants, USH2A gene p. Trp4175Arg, p.Cys575Arg, p.Phe625Leu and CYP4V2 gene p. Leu481Phe, are all pathogenic or harmful.Conservation analysis showed that they are conserved in multiple species.The prediction software spliceAI and varSEAK suggested that MERTK gene c.2487-8A>G may lead to abnormal shear and affect protein function. PCDH15 gene c. 5183del(p.Arg1728LysfsTer116) is a frameshift variant that alters the downstream amino acid sequence and terminates translation early. CYP4V2, USH2A, and RPGR were frequently mutated genes in RP patients, accounting for more than 50% of the families with pathogenic genes detected.The proband with CYP4V2 variants had late onset, but severe visual impairment and retinal degeneration.

Conclusions  Six previously unreported variants may be novel pathogenic variants of RP. CYP4V2, USH2A, and RPGR may be the most common pathogenic genes in Chinese RP patients.Patients with CYP4V2 variants have late onset, but faster disease progression.

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