Association of a Novel Intronic Variant in RPGR With Hypomorphic Phenotype of X-Linked Retinitis Pigmentosa

Abstract

IMPORTANCE Pathogenic variants in retinitis pigmentosa GTPase regulator (RPGR) gene typically lead to a severe form of X-linked retinitis pigmentosa, which is associated with early severe vision loss.OBJECTIVE To investigate an X-linked retinal degeneration family with atypical preservation of visual acuity in the presence of a novel deep intronic splice site RPGR c.779-5T>G variant. DESIGN, SETTING, AND PARTICIPANTSIn this case series, 3 members of an X-linked retinal degeneration family were studied by in-depth phenotyping and genetic screening at a single center. Data were collected and analyzed from November 2018 to March 2020.MAIN OUTCOMES AND MEASURES Data were collected on full ophthalmic history, examination, and retinal imaging. A full retinitis pigmentosa gene panel was analyzed by next-generation sequencing. The pathogenicity of the RPGR c.779-5T>G variant was assessed by in silico splice prediction tools and by purpose-designed in vitro splicing assay.RESULTS An 84-year-old man was referred with clinical diagnosis of choroideremia and possible inclusion into a gene therapy trial. He presented with late-stage retinal degeneration and unusually preserved visual acuity (78 and 68 ETRDS letters) that clinically resembled choroideremia. His 23-year-old grandson was still in early stages of degeneration but showed a very different clinical picture, typical of retinitis pigmentosa. Next-generation sequencing identified a sole RPGR c.779-5T>G variant of undetermined pathogenicity in both cases. The daughter of the proband showed an RPGR carrier phenotype and was confirmed to carry the same variant. The molecular analysis confirmed that the RPGR c.779-5T>G variation reduced the efficiency of intron splicing compared with wild type, leading to a population of mutant and normal transcripts. The predicted consequences of the pathogenic variant are potential use of an alternative splice acceptor site or complete skipping of exon 8, resulting in truncated forms of the RPGR protein with different levels of glutamylation.CONCLUSIONS AND RELEVANCE These results support the importance of careful interpretation of inconsistent clinical phenotypes between family members. Using a molecular splicing assay, a new pathogenic variant in a noncoding region of RPGR was associated with a proportion of normal and hypomorphic RPGR, where cones are likely to survive longer than expected, potentially accounting for the preserved visual acuity observed in this family.

X-Linked Retinitis Pigmentosa Caused by Non-Canonical Splice Site Variants in RPGR

“…We hypothesize that two disease entities run in the pedigree, namely XRP caused by a pathogenic RPGR allele and inherited through the maternal line, and ARRP caused by two pathogenic USH2A alleles inherited through both the maternal and the paternal line. This may explain the much more severe phenotype of our patient when compared to the patient described in the aforementioned study [ 19 ].…”

“…However, the consequence of the variants was not validated, and clinical details were not provided [ 18 ]. Very recently, variant c.779-5T>G was reported in another study and linked to a hypomorphic phenotype of XRP [ 19 ]. Splicing analysis of the variant based on a reporter construct showed a reduced efficiency of intron splicing compared with the wildtype [ 19 ].…”

“…We hypothesize that variants c.247 + 5G>A and c.779-5T>G influence the binding of RPGRIP1 and PDE6δ to the RCC1-like domain. As mentioned above, variant c.779-5T>G has been analyzed in a previous study and linked to a hypomorphic phenotype of XRP [ 19 ]. The index patient in the previous study presented with good visual acuity at age 84 years and a fundus appearance that resembled choroideremia [ 19 ].…”

“…As mentioned above, variant c.779-5T>G has been analyzed in a previous study and linked to a hypomorphic phenotype of XRP [ 19 ]. The index patient in the previous study presented with good visual acuity at age 84 years and a fundus appearance that resembled choroideremia [ 19 ]. The phenotype of our patient XRP 232, who harbors the c.779-5T>G variant, is much more severe.…”

Human iPSC-Derived Retinal Organoids and Retinal Pigment Epithelium for Novel Intronic RPGR Variant Assessment for Therapy Suitability

“…Variants in exon 1-14 and the proximal part of ORF15 are more frequently associated with rod-dominated disease, while those more in the 3′ region of ORF15 are more commonly associated with a cone or cone–rod phenotype [ 6 ]. Splice variants generally reflect this pattern, with studies indicating that correct splicing of both isoforms is integral for normal RPGR function [ 8 , 9 , 10 ].…”