Homozygosity mapping reveals novel and known mutations in Pakistani families with inherited retinal dystrophies

Abstract

Inherited retinal dystrophies are phenotypically and genetically heterogeneous. This extensive heterogeneity poses a challenge when performing molecular diagnosis of patients, especially in developing countries. In this study, we applied homozygosity mapping as a tool to reduce the complexity given by genetic heterogeneity and identify disease-causing variants in consanguineous Pakistani pedigrees. DNA samples from eight families with autosomal recessive retinal dystrophies were subjected to genome wide homozygosity mapping (seven by SNP arrays and one by STR markers) and genes comprised within the detected homozygous regions were analyzed by Sanger sequencing. All families displayed consistent autozygous genomic regions. Sequence analysis of candidate genes identified four previously-reported mutations in CNGB3, CNGA3, RHO, and PDE6A, as well as three novel mutations: c.2656C > T (p.L886F) in RPGRIP1, c.991G > C (p.G331R) in CNGA3, and c.413-1G > A (IVS6-1G > A) in CNGB1. This latter mutation impacted pre-mRNA splicing of CNGB1 by creating a -1 frameshift leading to a premature termination codon. In addition to better delineating the genetic landscape of inherited retinal dystrophies in Pakistan, our data confirm that combining homozygosity mapping and candidate gene sequencing is a powerful approach for mutation identification in populations where consanguineous unions are common.

Clinical Characterization of CNGB1-Related Autosomal Recessive Retinitis Pigmentosa

“…Of the 4 families with clinical detail, there was a childhood onset of nyctalopia with a later development of peripheral visual field loss reported in 4 patients at ages 10, 20 and 30 (2 patients) years. 10,15,17,19 Severe loss of visual acuity was present in of RP patients that have shown spatial correspondence or correlation between these parameters. 27,28 Central subfield thickness was within normal limits.…”

“…There are limited published data of the CNGB1 retinal phenotype. 10,[15][16][17][18][19][20] To our knowledge, only 7 families have been identified with recessive RP due to CNGB1 comprising 3 missense variants, 3 splice site variants and 1 frameshift variant. Of the 4 families with clinical detail, there was a childhood onset of nyctalopia with a later development of peripheral visual field loss reported in 4 patients at ages 10, 20 and 30 (2 patients) years.…”

“…Of the previously reported patients with clinical detail, 2 had splice site variants (c.413-1G>A and c.3444+1G>A) and visual loss at ages 24 and 67 years respectively; with missense variants had preserved central vision in to at least their 4 th decades. 10,15,17,19 The splice site variants have both been shown in vitro to lead to aberrant splicing and premature termination codons. 19,30 At this time, there is no demonstrable genotype-phenotype correlation.…”

“…10,15,17,19 The splice site variants have both been shown in vitro to lead to aberrant splicing and premature termination codons. 19,30 At this time, there is no demonstrable genotype-phenotype correlation.…”

“…13,14 Variants in CNGB1 are an uncommon cause of RP, accounting for approximately 4% of arRP cases; there are limited reports describing the associated phenotypes. 10,[15][16][17][18][19][20] The present report describes the detailed clinical features of ten affected patients harboring likely pathogenic variants in CNGB1.…”