Abstract
Purpose :
Advances in research and high-throughput sequencing technologies have transformed the process of uncovering causal genes for Mendelian disorders. Despite this, many causal variants are elusive, leaving 30-40% of inherited retinal degeneration (IRD) cases unsolved. For this reason, we reexamined our IRD cohort at Massachusetts Eye and Ear for previously overlooked solutions in newly discovered and known IRD genes.
Methods :
Previously generated targeted, exome, and genome sequence data from over 3000 IRD cases were reanalyzed with updated bioinformatic pipelines (GATK and GATK-SV) to detect single nucleotide variants, small indels and structural variants. Mendelian Analysis Toolkit and an online platform (seqr.broadinstitute.org) were used to prioritize likely causal variants. The variants were confirmed by PCR and Sanger sequencing in probands and available family members. For selected cases, mRNA was extracted from peripheral blood, where RT-PCR and qPCR was performed to investigate the potential effect of variants on pre-mRNA splicing.
Results :
We identified 5 rod-cone dystrophy cases carrying rare likely causal variants in the Pre-mRNA Processing Factor-31 (PRPF31) gene, that were originally overlooked because in the initial analysis the cases were considered as recessive, due to the incomplete penetrance present in one of the parents. Three variants were missense changes: c.1140C>G, p.Phe380Leu, c.757G>C, p.Gly253Arg, c.829A>C, p.Ser277Arg, and two variants were intronic: c.946-12 C>A, and c.856-2 A>G. The variants are absent in the gnomAD v4.0.0 variant database, are highly conserved, and predicted to be probably damaging by multiple in silico predictors, including the Evolutionary Model of Variant Effect (>0.9).
Conclusions :
We present novel likely pathogenic missense and intronic variants in PRPF31. Our study shows a value of genetic data reanalysis to reduce missed diagnosis due to the analyst bias and to keep up with the constantly improving annotation sources, next generation sequencing processing pipelines and newly discovered IRD genes.
This abstract was presented at the 2024 ARVO Annual Meeting, held in Seattle, WA, May 5-9, 2024.