Inherited retinal diseases (IRDs) are a diverse group of disorders that share common vision deficit ranging from early onset blindness to seInherited retinal diseases (IRDs) are a diverse group of disorders that share common vision deficit ranging from early onset blindness to severe and progressive blindness occurring in later years. We report a form of cone-rod dystrophy with early onset day vision loss in the Standard poodle. Through GWAS and homozygosity mapping, a large deletion on CFA8:g.(60,022,583_60,040,453del) was found, which removes 3’ portions of two different genes, PTPN21 and SPATA7, presenting a challenge for assessing the actual causative gene in a multi-gene large deletion. All affected dogs were homozygous for the mutant allele, which segregated perfectly with the phenotype within the breed. The variant was also absent fromand was also absent in more than control canine structural variants database(dog10k). While the role of SPATA7 for retinal disease has been established in human patients and genetically engineered mice, the role of PTPN21 in retina is unclear even though it is expressed in rod and cone photoreceptors. Expression of truncated transcripts for both genes was detected in skin fibroblasts from the cases. Retinal RNA analysis showed that PTPN21 splicing suggests that in mutant dogs at least one unmodified transcript is present. Ptpn21^-/- knockout mice did not have an ocular phenotype, and opsin-specific IHC detected no cone or rod abnormalities in the mice suggesting that PTPN21 loss has none to minimal contributory role towards the retinal phenotype in the affected dogs. The SPATA7 deletion (XM_038674407.1:c.1,301-2,070del, p.Arg387_Asp595del) affects the coding region of the transcript, reducing the predicted protein from 595 to 386 AA . Ultrastructure expansion microscopy (U-ExM) enabled the detection of a distinct SPATA7 signal around the transition zone of the primary cilium in WT canine-skin fibroblasts, which was absent in that of affected dogs. We propose that SPATA7 deficiency is the main cause of the condition and propose this disease as a model for the SPATA7-related form of cone-rod dystrophy in human. Our work shows an example of functional refinement of a multi-gene deletion variant using a multi-technique approach.

SNPdata: genotype data Type from 170k and 220k CanineHD array (Illumina). DNA was extracted from blood. Processed: Neogen.

SP03 NovaSeq6000 paired-end reads (2x100 bp) whole genome sequencing (as for company instructions). The PCR-free library was prepared as follows. Libraries of 300 bp insert size were prepared, and Illumina NovaSeq6000 paired-end reads (2 × 100 bp) were collected. Fastq files were generated using Casava.