DOI: 10.5061/dryad.59zw3r2b7
title: Analysis of rod-cone dystrophy genes reveals unique mutational patterns

description: Background Rod-cone dystrophy (RCD) is the most common inherited retinal
 disease that is characterised by the progressive degeneration of retinal
 photoreceptors. RCD genes' classification is based exclusively on
 gene mutations’ prevalence and does not consider the implication of the
 same gene in different phenotypes. Therefore, we first investigated the
 mutations occurrence in autosomal recessive RCD (arRCD) and non-arRCD
 conditions. Then, finally, we identified arRCD enriched mutational
 patterns in specific genes and coding exons. Methods and results The
 mutations' patterns differed according to arRCD (p=0.001).
 Specifically, When compared with missense; insertions/deletions (OR=1.2,
 p=0.007), nonsense (OR=1.2, p=0.014) and splice-site mutations (OR=1.6,
 p=0.038) increased the OR of arRCD by 20%–60% versus non-arRCD conditions.
 The gene-based analysis identified that EYS, IMPG2, RP1L1 and USH2A
 mutations were enriched in arRCD (p&lt;0.05). The exon-based analysis
 revealed specific mutation patterns in exons of CRB1, RP1L1 and exons 12,
 60 and 62 coding for Lamin EGF and FTIII domains of USH2A. Conclusion The
 current analysis showed that many aRCD genes have unique mutational
 patterns.
description: Data extraction, inclusion, and exclusion criteria
 The Retinal Information Network Database The
 Retinal Information Network (Retnet) is a database that provides tables of
 genes and loci causing IRDs (https://sph.uth.edu/retnet/). Thus, it was used to search the arRCD genes. In total, sixty-three genes were found (<em>ABCA4, AGBL5, AHR, ARHGEF18, ARL6, ARL2BP, BBS1, BBS2, BEST1, C2orf71, C8orf37, CERKL, CLCC1, CLRN1, CNGA1, CNGB1, CRB1, CYP4V2, DHDDS, DHX38, EMC1, EYS, FAM161A, GPR125, HGSNAT, IDH3B, IFT140, IFT172, IMPG2, KIAA1549, KIZ, LRAT, MAK, MERTK, MVK, NEK2, NEUROD1, NR2E3, NRL, PDE6A, PDE6B, PDE6G, POMGNT1, PRCD, PROM1, RBP3, REEP6, RGR, RHO, RLBP1, RP1, RP1L1, RPE65, SAG, SAMD11, SLC7A14, SPATA7, TRNT1, TTC8, TULP1, USH2A, ZNF408, ZNF513</em>) (last accessed on June, 10, 2021). HGMD database Our sample population is individuals affected with rod-cone dystrophy. The genotype of these individuals was determined through various genotyping and sequencing techniques (genotyping arrays) such as next-generation sequencing (targeted and whole exome) and Sanger sequencing. Genetic variations in the sixty-three arRCD genes were downloaded in .txt format, with information including c.DNA position, protein position, class, associated phenotype, and corresponding reference (N=7,382). Mutations associated with 'retinal dystrophy' or 'retinal degeneration' and ‘retinal disease’ were not included in the analysis since these terms are broad and do not allow a correct diagnosis. This led to a total of 6,627 mutations (http://www.hgmd.cf.ac.uk/ac/index.php, accessed: September 10, 2021). We have removed the Rhodopsin mutations that were reported to have a dominant effect. Furthermore, we have removed the ‘duplicate’ mutations; these are different DNA mutations that lead to the same amino acid exchange in a gene. This filtering kept 5,868 mutations. For every mutation, we added a type (missense, nonsense, insertion/deletion (InDel), or splice site) based on the HGMD annotation. LOVD database Genetic variations in arRCD genes were also downloaded from the LOVD database (N=1,104; https://www.lovd.nl/, accessed: September 20,2021). UniProt and Gene databases All amino acid (a.a) domains were retrieved from the Uniprot database https://www.uniprot.org/. On the other hand, the longest mRNA isoform from the NCBI gene database was selected (http://www.ncbi.nlm.nih.gov/gene). Statistical analyses The analyses were conducted using SPSS software version 20 (SPSS, Inc., IL, USA). All studied variables were expressed as frequencies. The plots were generated using Origin software (OriginPro, Version 8, OriginLab Corporation, Northampton, MA, USA). Mutations distribution stratified according to autosomal recessive rod-cone dystrophy The number of unique mutations in HGMD database was compared according to arRCD phenotype (arRCD vs. non arRCD). Data from the LOVD database was used in the analysis of the total mutations only. Individual mutations and not their frequencies were used in the distribution analysis, and thus even if more than one affected individual carried a mutation, it was counted once. However, the genetic heterogeneity at the mutational level was considered. Thus, the mutations causing more than one phenotype were counted more than once according to their number of associations. The chi-square (χ<sup>2</sup>) goodness of fit test was used to compare the mutations number (in global, per gene, and per exon) according to arRCD.
description: Microsoft Excell and SPSS