X-linked Retinitis Pigmentosa (XLRP) via the RPGR Gene

Retinitis pigmentosa (RP) refers to a group of related eye disorders stemming from the degeneration of photoreceptor cells in the retina (Pagon and Daiger, 2005). RP derives its name from retinal pigmentation changes. In RP patients, pigment granules accumulate in perivascular clusters, called bone-spicules, in the retinal pigment epithelium (RPE). The accumulation of pigment is typically accompanied by death of the photoreceptor cells, first rods and eventually cones. As a result, RP will often present first with night blindness and decreased peripheral vision due to systematic loss of rod cells, followed by deterioration of central vision acuity and day blindness from the loss of cone cells. RP has an incidence of ~1/3500 and can be inherited in autosomal recessive, autosomal dominant, X-linked, digenic, and even mitochondrial patterns. Currently, variants in over 30 genes are known to cause RP.

X-linked RP (XLRP) is one of the most severe forms of RP, with early onset and rapid progression in males. Milder symptoms can also present in females, probably due to random X inactivation. At least five different genetic loci have been associated with XLRP: Xp11.2 (RP2), Xp21.1 (RPGR), Xp21.2-21.3 (RP6), Xp22 (RP23), and Xp26-27 (RP24) (http://www.sph.uth.tmc.edu/RetNet/disease.htm). To date, only the RP2 and RPGR genes have been identified. RPGR encodes the retinitis pigmentosa GTPase regulator (Meindl et al. 1996), and RP2 encodes a protein of unknown function. Variants in RPGR account for the vast majority (~80%) of all XLRP cases, with RP2 accounting for about 10% of cases and the other loci likely accounting for the remainder (~10%) (Breuer et al. 2002; Sharon et al. 2003). Males hemizygous for RPGR variants typically display classic features of RP, such as initial night blindness and loss of peripheral vision. However, RPGR variants have also been detected in patients presenting with cone dystrophy (Yang et al. 2002; Demirci et al. 2002) or atrophic macular degeneration (Ayyagari et al. 2002). The RPGR gene encodes several alternatively spliced isoforms, although RP-causing variants are only found in isoform C (CCDS35229.1). Isoform C consists of 15 coding exons, with exon 15 (usually referred to as ORF15; see Bader et al. 2003 for a detailed description of ORF15) coding for nearly 50% of the protein. Accordingly, variants in ORF15 account for ~50% of all XLRP cases (Vervoort et al. 2000; Sharon et al. 2003).

This test is predicted to detect a causative variant in ~70-80% of all patients with presumptive XLRP (Sharon et al. Am J Hum Genet 73:1131-1146, 2003; Hong et al. Invest Ophthalmol Vis Sci 46:435-441, 2005) or ~45% of patients with X-linked cone dystrophy (Demirci et al. Am J Hum Genet 70:1049-1053, 2002). The sensitivity for X-linked atrophic macular degeneration is unknown.

This test provides full coverage of all coding exons of the RPGR gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Analysis of RPGR exon 15 (commonly referred to as ORF15) has historically been difficult due to the highly repetitive, purine-rich sequence. When NGS does not achieve full coverage or there is a variant detected by NGS that needs confirmation, then we utilize a specialized chemistry Sanger sequencing.

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).

Targeted testing strategy for exons 1 to 14 For exons through 1 to 14, we will also sequence any single exon (Test #100) or pair of exons (Test #200) in family members of patients with known variants or to confirm research results.

Targeted testing strategy for exon 15 (ORF15) We will sequence ORF15 (Test #2085, $440) for clients who want to test this entire region.