A systematic review of inherited retinal dystrophies in Pakistan: updates from 1999 to April 2023

Inherited retinal dystrophies (IRDs) are a group of clinically and genetically diverse eye disorders ranging in prevalence from 1 in 2000 to 1 in 4000 people globally [1, 2]. IRDs are broadly divided into two categories (i) non-syndromic, and (ii) syndromic types depending upon absence or presence of extra-ocular manifestations, respectively. Major clinical symptoms of non-syndromic IRDs include, but not limited to, night blindness or nyctalopia, color vision deficiency, photophobia, nystagmus, reduced visual acuity, day vision loss as well as central or peripheral vision loss. Syndromic IRDs, on the other hand, are known for systemic findings such as obesity, polydactyly, renal abnormalities, deafness, speech, and intellectual disability together with ocular symptoms [3‐6]. Globally, mutations in over 300 distinct genes have thus far been associated with all forms of IRDs [3]. IRDs follow all modes of Mendelian inheritance such as autosomal recessive [7], autosomal dominant [8], X-linked [9], mitochondrial [10] as well as digenic [11] and oligogenic patterns [12]. Accordingly, IRDs are classified into various subtypes depending upon disease onset, mode of inheritance, rate of disease progression, clinical presentation, part of retina affected (rods, cones, retinal pigment epithelium, inner retina and choroid), and/or involvement of extra ocular phenotypes [13]. Non-syndromic and syndromic IRDs are briefly explained in the following sections.

This review was carried out between November-2022 and April-2023 by following PRISMA guidelines as mentioned in Supplementary Table S1. Briefly, the inclusion criteria for considering genetic studies comprised families of Pakistani descent, exhibiting both syndromic and non-syndromic inherited retinal disorders, and articles published during the period spanning from 1999 to April-2023. A thorough literature survey was performed for this purpose using PubMed (NCBI), Google Scholar, and Web of Science. Different key words such as inherited retinal degenerations/dystrophies, IRDs, retinitis pigmentosa (syndromic/non-syndromic), Stargardt disease, cone- and/or cone-rod dystrophy, macular degeneration, congenital stationary night blindness, leber congenital amaurosis, achromatopsia, color blindness, mutations, Pakistan, etc. were used for retrieving relevant literature. All articles that appeared during our search were further shortlisted and papers that did not fall under the purview of this review were excluded. This included articles presenting findings related to non-retinal phenotypes like cataract, age related macular dystrophy, microphthalmia, anophthalmia, aniridia, anterior segment dysgenesis, and sporadic cases. Data pertaining to genetic and clinical aspects of the families were extracted from all papers and recorded (and tabulated) in Microsoft (MS) excel sheet. This followed manual curation of the data using different options of the MS excel tool. Genomic nomenclature of all variants reported in this study were validated using VariantValidator [https://​variantvalidator​.​org]. Additional features of the variants such as impact of the variations on cDNA and protein level, gene symbols, protein and transcript ID, genomic coordinates of the variation, inheritance pattern, and allele frequencies were determined using major genomic data bases (Ensemble, UCSC, HGNC, OMIM, gnomAD). All identified variants were queried in different online databases such as ClinVar, HGMD and Varsome to check their clinical significance. ACMG verdicts about the variants were retrieved from Varsome database. Retinal information network (RetNet) was used to calculate number of genes associated with each IRDs type. All missense variants were evaluated for their predicted pathogenicity using different in-silico tools, namely, CADD, DANN, LRT, Mutation Assessor, Mutation Taster, Mutpred, PolyPhen-2, PROVEAN, and SIFT.

This study provides an overview of the existing clinical and genetic aspects of IRDs in Pakistani families based on published reports. Majority of the IRDs families in the published reports belonged to two major ethnic Pakistani populations i.e. Punjab and Khyber Pakhtunkhwa. Other ethnic Pakistani populations such as Sindh, Baluchistan and Gilgit-Baltistan were only marginally represented in the available medical literature. Consistent with the traditional practice of endogamy in the country [79‐81], over 70% IRDs cases in this study were found among children whose parents were consanguineously married. Consequently, recessively inherited IRDs were disproportionately high (> 95%) in the current report as opposed to dominant cases. Our findings reiterate the fact that consanguinity-driven homozygosity mapping can greatly leverage identification of novel disease genes in recessively inherited Mendelian disorders in endogamous populations as previously shown [82, 83]. For example, at least 12 IRDs-associated genes have been first identified/reported in Pakistani families [84, 85].

Of the total retrieved variants detected in IRDs families of Pakistani origin, ~ 80% were considered as ‘rare’ since they were reported only once from the Pakistani population. The remainder ~ 20% variants were observed at least twice in Pakistani families, hence they were considered as ‘recurrent’ alleles. Of the recurrent alleles, a frameshift mutation in LCA5 gene (NM_001122779.3:c.1151delC;p.Pro384GlnfsTer18) was independently reported seven times [76, 86‐91], and thus considered to be the topmost commonly reported allele in Pakistan.

While ethnic affiliations of index cases carrying c.1151delC allele were not provided in five out of seven studies, c.1151delC allele was independently reported in two unrelated families from KPK and Punjab provinces. The second most recurrent allele was a missense substitution (c.1138A > G:p.Thr380Ala) in the TULP1 (NM_003322.6) gene which was reported by five independent studies. Of them, two families belonged to ethnically matched KPK population, and thus possibly related. However, one family carrying c.1138A > G allele belonged to Punjab province. No data on the ethnic affiliation was available in the remaining two reports [88‐90, 92, 93]. In addition to the likelihood that these alleles constitute hotspot mutations, frequent occurrence of these recurrent alleles in multiple and ethnically matched Pakistani families might indicate a founder effect in the society.

Our findings, of RP as the most leading IRD type in Pakistani families (41%), align with several previous studies suggesting RP as the most frequently reported form of IRDs in world populations [94‐98]. Also, we have found that RP is the most genetically heterogeneous disorder among IRDs in Pakistani population as mutations in 37 different RP-associated genes were identified. Nonetheless, Pakistani families somehow present unique genetic architecture of IRDs. For example, unlike ABCA4 and/or USH2A gene mutations which are considered as a major etiology of the IRDs cases worldwide [96‐98], we have found that PDE6A gene mutations are the leading cause of IRDs in Pakistani families. While disease-causing mutations in SNRNP200 gene are known to cause adRP [99‐101], SNRNP200 gene mutation correlated with arRP in a Pakistani IRD family [102]. Lastly, detection of rare forms of IRDs notably STX3-associated intestinal-retinal syndrome [103], VPS13B-associated Cohen syndrome [104], and SLC6A6-associated taurine transporter (TauT) deficiency disorders [105] in Pakistani families not only points towards the distinctive genetic nature of this population but it also highlights its potential in medical research.

Our CADD score analysis of all missense variants that are described in this report revealed two alleles with lowest CADD-PHRED scores. These included RP1 (c.2005G > A; p.Ala669Thr), and RAX2 (c.374G > A; p.Gly125Glu) with a CADD-PHRED scores of 1.173 and 1.497, respectively. Though our in-silico findings about these alleles are not final, we recommend further researcher to further investigate these two missense variants in order to fully characterize their impact on protein structure and/or function.

This study provides a comprehensive overview of IRDs in Pakistani families over a period of 25 years (1999–2023). Our analysis reaffirms the fact that majority of the prevalent IRDs cases in Pakistan are recessively inherited, and that they mostly appeared due to the bi-allelic inheritance of rare pathogenic mutations from both parents. Undoubtedly, RP was the most frequently occurring IRD in Pakistan followed by LCA. Overall, PDE6A gene mutations was the leading cause of IRDs in Pakistani families followed by mutations in TULP1 gene. Altogether, marked genetic and allelic and heterogeneity was observed in the Pakistani IRDs families. In summary, Pakistani families are notable in expressing both common and rare Mendelian disorders such as Cohen syndrome, intestinal-retinal syndrome, and taurine transporter deficiency possibly due to the traditional practice of endogamy in the society.