Prevalence of RPGR-Mediated Retinal Dystrophy in an Unselected Cohort of Over 5000 Patients

Abstract

Purpose Comprehensive genetic testing for inherited retinal dystrophy (IRD) is challenged by difficult-to-sequence genomic regions, which are often mutational hotspots, such as RPGR ORF15. The purpose of this study was to evaluate the diagnostic contribution of RPGR variants in an unselected IRD patient cohort referred for testing in a clinical diagnostic laboratory. Methods A total of 5201 consecutive patients were analyzed with a clinically validated next-generation sequencing (NGS)–based assay, including the difficult-to-sequence RPGR ORF15 region. Copy number variant (CNV) detection from NGS data was included. Variant interpretation was performed per the American College of Medical Genetics and Genomics guidelines. Results A confirmed molecular diagnosis in RPGR was found in 4.5% of patients, 24.0% of whom were females. Variants in ORF15 accounted for 74% of the diagnoses; 29% of the diagnostic variants were in the most difficult-to-sequence central region of ORF15 (c.2470-3230). Truncating variants made up the majority (91%) of the diagnostic variants. CNVs explained 2% of the diagnostic cases, of which 80% were one- or two-exon deletions outside of ORF15. Conclusions Our findings indicate that high-throughput, clinically validated NGS-based testing covering the difficult-to-sequence region of ORF15, in combination with high-resolution CNV detection, can help to maximize the diagnostic yield for patients with IRD. Translational Relevance These results demonstrate an accurate and scalable method for the detection of RPGR -related variants, including the difficult-to-sequence ORF15 hotspot, which is relevant given current and emerging therapeutic opportunities.

Genetic Characteristics and Long-Term Follow-Up of Slovenian Patients with RPGR Retinal Dystrophy

“…Of those in the database, the majority (75%) are truncation variants (frameshift 54%; stop variants 21%), whereas missense variants are in the minority (21%). Even higher percentages of truncating variants (84%) were reported in a systematic analysis that included 585 RPGR variants [ 41 ] as well as in a study that included 234 RPGR patients (89%; of those 69% (161/234) were frameshift and 20% were nonsense) [ 42 ], which was consistent with our findings.…”

“…In a systematic analysis, the rare missense and in-frame variants were found to be enriched in the regulator of the chromosome condensation (RCC1)-like domain [ 41 ], a tandem repeat structure that resides in the region between exons 3 and 10 (amino acid residues 54–367) [ 44 ]. Accordingly, all diagnostic missense variants in the study by Tuupanen S et al were also located within that region, and the Slovenian novel missense variant p.Ala153Thr resided in the 5th exon, which further corroborated this observation [ 42 ].…”

“…Between 60 and 80% of disease-causing variants in RPGR are found in the ORF15 exon [ 22 , 42 , 43 ]. Exon ORF15 is the longest exon of RPGR and contains 567 amino acids or approximately half (567/1152 amino acid residues) of the total length of the main RPGR isoform.…”

“…Approximately 20–30% of the pathogenic variants are located in the most difficult-to-sequence central region of ORF15 (c.2470-3230; p. 824–p. 1077) [ 42 ].…”

“…The frequency of different RPGR variants varied in different cohorts. For example, the most commonly observed pathogenic variants in the study by Tuupanen S and colleagues, which included 234 RPGR patients of different ethical origins (United States—86%, Canada—9%, Europe—4.5%, Latin America—0.2%, the Middle East—0.4%, and the South Pacific—0.2%), were p.(Glu802Glyfs*12) (20/234 cases, 9%), p.(Glu746Argfs*23) (12/234 cases, 5%), and p.(Glu809Glyfs*25) (10/234 cases, 4%), all of which resulted in RP [ 42 ]. In other cohorts; for example, a Chinese cohort described by Yang J and colleagues, the most commonly observed pathogenic variant was p.(Glu746Argfs*23) followed by p.(Glu802Glyfs*32) and p.(Glu1010Glyfs*68), all of which resulted in RP [ 41 ].…”