|Year : 2017 | Volume
| Issue : 3 | Page : 228-231
Novel PDE6A mutation in an Emirati patient with retinitis pigmentosa
Pratibha Nair1, Abdul Rezzak Hamzeh1, Ethar Mustafa Malik2, Darshjit Oberoi3, Mahmoud Taleb Al-Ali1, Fatma Bastaki2
1 Centre for Arab Genomic Studies, Dubai, UAE
2 Department of Pediatric, Latifa Hospital, Dubai Health Authority, Dubai, UAE
3 Department of Ophthalmology, Dubai Hospital, Dubai, UAE
|Date of Web Publication||5-Oct-2017|
Centre for Arab Genomic Studies, Dubai
Source of Support: None, Conflict of Interest: None
| Abstract|| |
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.
Keywords: Emirati, PDE6A, retinitis pigmentosa, whole-exome sequencing
|How to cite this article:|
Nair P, Hamzeh AR, Malik EM, Oberoi D, Al-Ali MT, Bastaki F. Novel PDE6A mutation in an Emirati patient with retinitis pigmentosa. Oman J Ophthalmol 2017;10:228-31
|How to cite this URL:|
Nair P, Hamzeh AR, Malik EM, Oberoi D, Al-Ali MT, Bastaki F. Novel PDE6A mutation in an Emirati patient with retinitis pigmentosa. Oman J Ophthalmol [serial online] 2017 [cited 2019 Jun 16];10:228-31. Available from: http://www.ojoonline.org/text.asp?2017/10/3/228/216001
| 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. Close to 60 different genes have so far been implicated in the pathogenesis of nonsyndromic RP. 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. 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.
Mutations in PDE6A were shown to result in a form of RP, designated as RP43 (OMIM#613810). 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, and/or increased accumulation of cGMP, either of which may lead to rod death.
|Table 1: Overview of PDE6A mutations reported in families with retinitis pigmentosa|
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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|
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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.
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 [Figure 2]a,[Figure 2]b,[Figure 2]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|
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| Discussion|| |
PDE6A includes two cGMP-specific phosphodiesterases, adenylyl cyclases, and FhlA (GAF) domains and a cyclic nucleotide phosphodiesterase domain [Figure 2]d. 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 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,, 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
Conflicts of interest
There are no conflicts of interest.
| References|| |
Zhang Q. Retinitis pigmentosa: Progress and perspective. Asia Pac J Ophthalmol (Phila) 2016;5:265-71.
Daiger SP, Sullivan LS, Bowne SJ. Genes and mutations causing retinitis pigmentosa. Clin Genet 2013;84:132-41.
Cote RH. Characteristics of photoreceptor PDE (PDE6): Similarities and differences to PDE5. Int J Impot Res 2004;16 Suppl 1:S28-33.
Matte SL, Laue TM, Cote RH. Characterization of conformational changes and protein-protein interactions of rod photoreceptor phosphodiesterase (PDE6). J Biol Chem 2012;287:20111-21.
Huang SH, Pittler SJ, Huang X, Oliveira L, Berson EL, Dryja TP. Autosomal recessive retinitis pigmentosa caused by mutations in the alpha subunit of rod cGMP phosphodiesterase. Nat Genet 1995;11:468-71.
Fain GL, Lisman JE. Light, Ca2+, and photoreceptor death: New evidence for the equivalent-light hypothesis from arrestin knockout mice. Invest Ophthalmol Vis Sci 1999;40:2770-2.
Sahaboglu A, Paquet-Durand O, Dietter J, Dengler K, Bernhard-Kurz S, Ekström PA, et al.
Retinitis pigmentosa: Rapid neurodegeneration is governed by slow cell death mechanisms. Cell Death Dis 2013;4:e488.
Chebil A, Falfoul Y, Habibi I, Munier F, Schorderet D, El Matri L. Genotype-phenotype correlation in ten Tunisian families with non-syndromic retinitis pigmentosa. J Fr Ophtalmol 2016;39:277-86.
Dryja TP, Rucinski DE, Chen SH, Berson EL. Frequency of mutations in the gene encoding the alpha subunit of rod cGMP-phosphodiesterase in autosomal recessive retinitis pigmentosa. Invest Ophthalmol Vis Sci 1999;40:1859-65.
Tsang SH, Tsui I, Chou CL, Zernant J, Haamer E, Iranmanesh R, et al.
A novel mutation and phenotypes in phosphodiesterase 6 deficiency. Am J Ophthalmol 2008;146:780-8.
Bocquet B, Marzouka NA, Hebrard M, Manes G, Sénéchal A, Meunier I, et al.
Homozygosity mapping in autosomal recessive retinitis pigmentosa families detects novel mutations. Mol Vis 2013;19:2487-500.
Riazuddin SA, Zulfiqar F, Zhang Q, Yao W, Li S, Jiao X, et al.
Mutations in the gene encoding the alpha-subunit of rod phosphodiesterase in consanguineous Pakistani families. Mol Vis 2006;12:1283-91.
Khan SY, Ali S, Naeem MA, Khan SN, Husnain T, Butt NH, et al.
Splice-site mutations identified in PDE6A responsible for retinitis pigmentosa in consanguineous Pakistani families. Mol Vis 2015;21:871-82.
Siemiatkowska AM, Arimadyo K, Moruz LM, Astuti GD, de Castro-Miro M, Zonneveld MN, et al.
Molecular genetic analysis of retinitis pigmentosa in Indonesia using genome-wide homozygosity mapping. Mol Vis 2011;17:3013-24.
Sothilingam V, Garcia Garrido M, Jiao K, Buena-Atienza E, Sahaboglu A, Trifunovic D, et al.
Retinitis pigmentosa: Impact of different Pde6a point mutations on the disease phenotype. Hum Mol Genet 2015;24:5486-99.
Corton M, Blanco MJ, Torres M, Sanchez-Salorio M, Carracedo A, Brion M. Identification of a novel mutation in the human PDE6A gene in autosomal recessive retinitis pigmentosa: Homology with the nmf28/nmf28 mice model. Clin Genet 2010;78:495-8.
Vaser R, Adusumalli S, Leng SN, Sikic M, Ng PC. SIFT missense predictions for genomes. Nat Protoc 2016;11:1-9.
Wolthuis DF, van Asbeck E, Mohamed M, Gardeitchik T, Lim-Melia ER, Wevers RA, et al.
Cutis laxa, fat pads and retinopathy due to ALDH18A1 mutation and review of the literature. Eur J Paediatr Neurol 2014;18:511-5.
Kariminejad A, Bozorgmehr B, Najafi A, Khoshaeen A, Ghalandari M, Najmabadi H, et al.
Retinitis pigmentosa, cutis laxa, and pseudoxanthoma elasticum-like skin manifestations associated with GGCX mutations. J Invest Dermatol 2014;134:2331-8.
[Figure 1], [Figure 2]