Primary Ciliary Dyskinesia (PCD) via the RPGR Gene

Primary ciliary dyskinesia (PCD) is a genetically heterogeneous disorder affecting the function of motile cilia (reviewed by Leigh et al. 2009). Motile cilia line the upper and lower respiratory airways, the ventricular system of the brain and spinal cord, and the female fallopian tubes. They are also components of the male sperm flagellum and required for sperm motility. Ciliary movement sweeps mucus, dirt, and bacteria out of the lungs, nasal passageways, and ear canals, thus protecting them from recurrent infections. In the developing embryo, nodal cilia generate a rotational motion that determines the position of the internal organs. Without functional nodal cilia, thoracoabdominal orientation is random. The hallmark features of PCD are neonatal respiratory distress, chronic coughing, and recurrent sinus or ear infections; 80-100% of all PCD patients have one or more of these symptoms. In about 50% of individuals with PCD, the major visceral organs are reversed from their normal positions (also called situs inversus or Kartagener’s syndrome). Fetal cerebral ventriculomegaly and hydrocephalus can also occur due to impaired circulation of the cerebrospinal fluid. In adults with PCD, male infertility and female sub-fertility are also common features. Prompt diagnosis of PCD is critical for the prevention of secondary respiratory complications, such as bronchiectasis, pneumonia, or progressive loss of lung function.

PCD is most often inherited in an autosomal recessive pattern. Occasionally, however, symptoms of PCD and retinitis pigmentosa (RP; OMIM 268000) co-segregate in an X-linked pattern (Zito et al. 2003; Moore et al. 2006). RPGR, located on the X chromosome, encodes the retinitis pigmentosa GTPase regulator (Meindl et al. 1996). Loss-of-function variants in RPGR can disrupt the structure of both photoreceptor-connecting clia and motile cilia (Hong et al. 2003), thus leading to a combined RP and PCD condition (Moore et al. 2006). Males hemizygous for RPGR variants often display early onset retinal degeneration, hearing loss, recurrent sinusitis, and chronic chest infections. Female carriers of heterozygous RPGR variants may also suffer from mild symptoms of PCD or RP, including late-onset retinal degeneration, recurrent sinusitis minus chest infections, and progressive hearing loss. The RPGR gene encodes several alternatively spliced isoforms. These include isoform A (CCDS14246.1), consisting of 19 exons, and isoform C (CCDS35229.1), consisting of 15 exons. Exons 1-14 are the same for both isoforms. However, isoform A uses a cryptic donor splice site in exon 15, resulting in a short (152 nucleotides) exon 15 and inclusion of exons 16-19. By contrast, isoform C does not use the cryptic donor splice site, resulting in an extended exon 15 (also called ORF15 in the literature) with 1706 nucleotides of coding sequence (see Bader et al. 2003 for a detailed description of the ORF15 exon). Importantly, because isoform C (with ORF15) is preferentially expressed in retina and isoform A (without ORF15) is expressed throughout the respiratory tract, variants in ORF15 lead to X-linked RP without symptoms of PCD while variants in exons 1-14 lead to XLRP with additional PCD symptoms.

This test is predicted to detect a causative variant in about 10% of patients with apparently X-linked PCD (Moore et al. J Med Genet 43:326-333, 2006), or ~50-60% of all patients diagnosed with X-linked RP (Bader et al. Invest Ophthalmol Vis Sci 44:1458-1463, 2003).

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).

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).