Whole Genome Sequencing of Giant Schnauzer Dogs with Progressive Retinal Atrophy Establishes NECAP1 as a Novel Candidate Gene for Retinal Degeneration

Canine progressive retinal atrophies (PRA) are genetically heterogeneous diseases characterized by retinal degeneration and subsequent blindness. PRAs are untreatable and affect multiple dog breeds, significantly impacting welfare. Three out of seven Giant Schnauzer (GS) littermates presented with PRA around four years of age. We sought to identify the causal variant to improve our understanding of the aetiology of this form of PRA and to enable development of a DNA test. Whole genome sequencing of two PRA-affected full-siblings and both unaffected parents was performed. Variants were filtered based on those segregating appropriately for an autosomal recessive disorder and predicted to be deleterious. Successive filtering against 568 canine genomes identified a single nucleotide variant in the gene encoding NECAP endocytosis associated 1 (NECAP1): c.544G>A (p.Gly182Arg). Five thousand one hundred and thirty canids of 175 breeds, 10 cross-breeds and 3 wolves were genotyped for c.544G>A. Only the three PRA-affected GS were homozygous (allele frequency in GS, excluding proband family = 0.015). In addition, we identified heterozygotes belonging to Spitz and Dachshund varieties, demonstrating c.544G>A segregates in other breeds of German origin. This study, in parallel with the known retinal expression and role of NECAP1 in clathrin mediated endocytosis (CME) in synapses, presents NECAP1 as a novel candidate gene for retinal degeneration in dogs and other species.

犬进行性视网膜萎缩（progressive retinal atrophy, PRA）是一类遗传异质性疾病，以视网膜变性及继发失明为特征。该类疾病目前尚无有效治疗方案，可累及多种犬品种，对动物福利造成显著不良影响。7只巨型雪纳瑞（Giant Schnauzer，以下简称GS）同窝个体中，有3只在约4岁时出现PRA症状。本研究旨在鉴定其致病变异，以加深对该类型PRA发病机制的理解，并助力DNA检测方法的开发。研究对2只患病的同胞全兄弟及2名未患病的亲本进行了全基因组测序。基于符合常染色体隐性遗传模式的分离规律，以及预测具有致病性的标准对变异位点进行筛选；通过对568份犬全基因组数据进行逐步筛选，最终在NECAP内吞作用相关1（NECAP endocytosis associated 1，以下简称NECAP1）基因中鉴定到1个单核苷酸变异：c.544G>A（p.Gly182Arg）。研究对175个犬品种、10个杂交品种及3只狼的共5130只犬科动物进行了c.544G>A位点的基因分型。仅3只患病的巨型雪纳瑞为纯合子（排除先证者家系后，巨型雪纳瑞群体中的等位基因频率为0.015）。此外，研究在史毕兹犬（Spitz）和腊肠犬（Dachshund）品种中鉴定到杂合携带者，证明c.544G>A变异在其他德国起源犬品种中存在分离现象。结合已知的NECAP1在视网膜中的表达特性，以及其在突触网格蛋白介导的内吞作用（clathrin mediated endocytosis，以下简称CME）中发挥的功能，本研究将NECAP1确定为犬及其他物种视网膜变性的新型候选基因。