Identification of a novel RPGRIP1 mutation in an Iranian family with leber congenital amaurosis by exome sequencing

Abstract

Leber congenital amaurosis (LCA) is a heterogeneous, early‐onset inherited retinal dystrophy, which is associated with severe visual impairment. We aimed to determine the disease‐causing variants in Iranian LCA and evaluate the clinical implications. Clinically, a possible LCA disease was found through diagnostic imaging, such as fundus photography, autofluorescence and optical coherence tomography. All affected patients showed typical eye symptoms associated with LCA including narrow arterioles, blindness, pigmentary changes and nystagmus. Target exome sequencing was performed to analyse the proband DNA. A homozygous novel c. 2889delT (p.P963 fs) mutation in the RPGRIP1 gene was identified, which was likely the deleterious and pathogenic mutation in the proband. Structurally, this mutation lost a retinitis pigmentosa GTPase regulator (RPGR)‐interacting domain at the C‐terminus which most likely impaired stability in the RPGRIP1 with the distribution of polarised proteins in the cilium connecting process. Sanger sequencing showed complete co‐segregation in this pedigree. This study provides compelling evidence that the c. 2889delT (p.P963 fs) mutation in the RPGRIP1 gene works as a pathogenic mutation that contributes to the progression of LCA.

A novel, homozygous nonsense variant of the CDHR1 gene in a Chinese family causes autosomal recessive retinal dystrophy by NGS‐based genetic diagnosis

“…The study consisted of a proband (Figure , pedigree II: 4, arrow), and 9‐related family members from three‐generations, with no consanguineous marriage history, based on their genetic and pedigree analysis (Figure ). For clinical diagnosis, a detailed clinical history and ophthalmic examinations were performed in proband, including the best‐corrected Snellen visual acuity, humphrey visual fields, ‎slit‐lamp biomicroscopy, fundoscopy, ‎optical coherence tomography, fundus photographs (FP) and fundus fluorenscent photographs (FFP), and standard electroretinography, which were used in previously studies …”

“…To access the disease‐causing genes and mutations, the panels for TES analyses on the DNA sample from the proband M341 were designed, according to the Illumina paired‐end libraries (Illumina, Inc., San Diego, CA, USA) . The capture Agilent probes were used in previously published studies . Two micrograms of extracted proband gDNA was randomly sonicated into 300~500 bp fragments.…”

“…Then hybridization to the pre‐capture libraries was quantified (the PicoGreen fluorescence assay kit, Invitrogen, Carlsbad, CA, USA). Each captured DNA libraries were applied for sequencing on Illumina HiSeq 2000 (Illumina, Inc.) at the BCM core facility, following the manufacturer's protocols, after pre‐capture libraries pooled, washed and recovered (Agilent Technologies, Santa Clara, CA, USA) . Then, paired‐end sequencing illumina reads were aligned to the human hg19 reference genome using Burrows‐Wheeler Aligner version 0.6.1 and available public online UCSC database (http://genome.ucsc.edu/).…”

A Novel Variant of the FZD4 Gene in a Chinese Family Causes Autosomal Dominant Familial Exudative Vitreoretinopathy

“…Only very rare variants were considered, with a dominant frequency cutoff of 0.05% [5]. Sequencing depth 4, estimated copy number 2, SNP quality 20, and a distance between two SNPs of>5 were used as the filtration criteria for candidate SNPs, according to previously reported studies [29,30]. Sequence variants should not be annotated in any of the above public databases.…”

“…For mutation verification and co-segregation analysis, polymerase chain reaction (PCR) amplification and direct Sanger sequencing of the variant were applied to gDNA of all available individuals [29,30]. A locus-specific primer pair (M362-FZD4) was designed using the online Primer3 program (http://primer3.…”