Novel PDE6A mutation in an Emirati patient with retinitis pigmentosa.

Mutations in the PDE6A gene are known to cause a form of retinitis pigmentosa (RP43), characterized by progressive retinal degeneration. We describe an Emirati patient with RP caused by a novel mutation in PDE6A. Clinical diagnosis of RP was made based on clinical evaluation and electroretinograms. The molecular analysis involved performing whole-exome sequencing, which enabled the identification of a homozygous 2-bp deletion (c.1358_1359delAT) in PDE6A, which was predicted to result in a frameshift and premature termination (p.Ile452Serfs*7). The mutation completely removed the catalytic PDEase domain in the protein. The parents were found to be heterozygous carriers of the variant. We thus report the first known case of a pathological variant in the PDE6A gene from the Arabian Peninsula.

Introduction

Retinitis pigmentosa (RP) is a clinically and genetically heterogeneous group of disorders characterized by progressive degeneration of the retina, resulting in profound vision loss or blindness. The rod photoreceptors are the first to be affected, followed by the cones. Clinically, the condition is characterized by night blindness, gradually reduced visual acuity, degenerative changes in the fundus, and macular degeneration. Both syndromic and nonsyndromic forms of RP exist.[1] Close to 60 different genes have so far been implicated in the pathogenesis of nonsyndromic RP.[2] One of these genes is PDE6A that codes for the cyclic guanosine monophosphate (cGMP)-specific phosphodiesterase 6A alpha subunit, expressed in cells of the retinal rod outer segment. One of these α subunits along with a β and two γ subunits go into the composition of the PDE6 holoenzyme tetramer, which is an important regulator of circulating cGMP levels in the outer rod segment. The cGMP levels, in turn, influence the rod cell membrane current, thereby triggering or suppressing signal transmission to the brain through the inner retina and the optic nerve.[3] In the dark, the PDE6A protein is inhibited by the binding of the γ subunits, and is thus inactive, which results in high cGMP levels within the retinal disc membranes. However, with illumination, the inhibitory subunits are removed from PDE6A through transducin, leaving it free to catalyze the hydrolysis of cGMP, resulting in a subsecond drop in their levels, and subsequent membrane hyperpolarization.[4]

Mutations in PDE6A were shown to result in a form of RP, designated as RP43 (OMIM#613810).[5] Till date, mutations in PDE6A have been reported in 20 families affected with RP [Table 1]. This condition is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Although the exact etiology of the rod–cone degeneration is not known, it has been hypothesized to be due to an increased Ca2+ influx,[6] and/or increased accumulation of cGMP,[7] either of which may lead to rod death.

Table 1

Overview of PDE6A mutations reported in families with retinitis pigmentosa

Here, we report a consanguineous Emirati family affected with RP with a novel mutation in PDE6A. This is the first mutation in the gene reported from the United Arab Emirates.

Case Report

An 8-year-old male patient was born to first cousin Emirati parents. He was referred to the genetics clinic with a diagnosis of RP and skin pigmentation problems. He had been completely normal till the age of 4 years, at which time he started to have problems seeing in the evening and was diagnosed with progressive night blindness. He was also found to have myopic astigmatism. On examination, he was found to be an alert and active boy, with no obvious dysmorphic features. Developmental history was appropriate for age. Detailed ocular examination revealed the following features: Right eye = −1 D/−1.75 × 15, left eye = −0.5 D/−2.5 × 150; visual acuity right eye = 1, left eye = 1, clear cornea, normal anterior chamber, and clear lens. The fundus bilaterally showed bone spicule pigmentation, attenuated arterioles, and pale optic discs. Visual evoked potential was within the normal range. Electroretinogram (ERG) was performed according to the ISCEV standards on a Tomey EP-1000 instrument. ERG revealed markedly reduced amplitudes for both N1 and P1 waves, signifying grossly affected rod function. Within the right eye, N1 amplitudes were more severely depressed than P1 amplitudes, whereas in the left eye, both waves were equally depressed. Cone function was also found to be reduced but was better than rod function [Figure 1]. The patient had deep pigmented itchy spots over his legs, arms, and trunk with multiple abscess formation. Skin biopsy was not performed, and topical treatment was advised. Hearing tests were normal as were renal function tests. All other systems were also normal.

Figure 1

Electroretinograms of both eyes showing the (a) rod and (b) cone response

Both parents were myopic and had Lasik performed. There was no other known family history of a similar condition. All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

Molecular analysis

Informed written consent was obtained and genomic DNA was extracted from the patient's and his parents’ blood using standard methods. Patient's DNA was subjected to whole-exome sequencing performed by Syngenics, Malaysia. The resulting variant call format file comprised of 89,562 variants, which were filtered based on quality, frequency, genomic position, protein effect, pathogenicity, and previous associations with vision loss. Given the positive consanguinity in the family, homozygous variants were screened for first, followed by heterozygous and hemizygous variants. Keeping in mind the sex of the proband, X-linked variants were also looked for.

Screening for homozygous variants in genes known to be associated with the phenotype resulted in the identification of only a single candidate variant. Screening for heterozygous and hemizygous variants in the same set of genes did not return any extra candidate variants. In addition, expanding the screen to include pathological variants in all genes also did not result in any more promising candidate variants. The single homozygous candidate variant identified was a 2-bp deletion – c.1358_1359delAT in exon 10 of PDE6A. Sanger sequencing confirmed the presence of this variant in homozygous form in the patient and heterozygous form in both parents [Figures 2a–c]. The variant was not found in the Exome Aggregation Consortium Browser, or in the GalaxC™ allele frequency database which contains >2.5 million unique Middle Eastern pathogenic mutations and variants.

Figure 2

(a-c) Sequence chromatograms showing the novel PDE6A variant in a homozygous state in the patient (a) and in a heterozygous state in each of the parents (b and c). (d) Line diagram showing the PDE6A protein with positions of the GAF and PDEase domains within

Discussion

PDE6A includes two cGMP-specific phosphodiesterases, adenylyl cyclases, and FhlA (GAF) domains and a cyclic nucleotide phosphodiesterase domain [Figure 2d]. The mutation in our patient is expected to result in a frameshift in the protein at position 452, leading to a premature termination of seven amino acid residues downstream. The translated protein is thus expected to be completely lacking the critical catalytic phosphodiesterase domain. SIFT-INDEL[17] classes the mutation as damaging, with a confidence score of 0.858, and also predicts that the mutation will induce nonsense-mediated decay of the protein.

Among the 18 mutations reported in families with RP43, all except one have a direct effect on either the GAF domains or the catalytic phosphodiesterase domain. In addition, a significant number of these mutations result in premature truncation of the protein [Table 1]. The mutation we report also results in a truncation of the protein that eliminates the catalytic domain. In addition, this mutation is also expected to cause a nonsense-mediated decay of the protein. Further functional studies could help in confirming the impact of this mutation.

Although RP has been associated in some patients with dermatological anomalies such as cutis laxa,[1819] mutations in PDE6A, specifically, have not so far been seen to associate with skin changes. It is likely that the skin pigmentation anomalies and abscess formation in our patient stem from variants in other unrelated gene(s) that need to be looked into.

In summary, we have described an Emirati family with RP caused by a novel mutation in PDE6A. To the best of our knowledge, this is the first report of a pathological variant in this gene from the Arabian Peninsula and broadens the spectrum of mutations in PDE6A reported in RP.

Financial support and sponsorship

Nil.

Conflicts of interest

There are no conflicts of interest.