A CACNA1F deletion causes X-linked progressive retinal atrophy in racing Greyhounds

Abstract

Purpose : Progressive retinal atrophy (PRA) is a group of heritable diseases in dogs marked by progressive retinal degeneration and eventual blindness that is analogous to retinitis pigmentosa (RP) in humans. Canine models of RP would be valuable for identifying novel genetic etiologies and developing new therapies. Racing Greyhounds diagnosed with PRA, with early vision impairment (1.5-4 years of age) and affecting mostly males (males n=39, females n=1) were identified. We aimed to identify inheritance patterns and the causal mutation.

Methods : Pedigree analysis was performed. Whole genome sequencing (WGS) was performed in 10 greyhounds (5 affected males, 2 putative carrier females, and 3 unaffected males) using Illumina Hiseq 4000 to ~30X coverage; 158 control canine genomes from various breeds without evidence of PRA were utilized. Association analysis using variant call format files generated from WGS was performed using PLINK. A list of 13 X-linked candidate genes based on known association with PRA in dogs and RP in humans was created. Integrated Genomics Viewer (IGV) was used to visualize the candidate genes for structural variants.

Results : The pedigree analysis indicated an X-linked inheritance pattern and identified a popular sire and putative founder with >4500 offspring. Association analysis on PLINK identified large regions of the canine X chromosome and no protein-coding variants. A 1,781 bp deletion within CACNA1F was identified on IGV which included exons 13 and 14 (of 48) and is predicted to cause in-frame amino acid loss (517-647 of 1967). CACNA1F is highly expressed in photoreceptors and encodes a multipass transmembrane protein that acts as an alpha-1 subunit of a voltage-dependent calcium channel. The deletion is predicted to remove 4 of 6 helical transmembrane segments in domain II of the 4 homologous domains (I-IV). Using PCR and in-silico genotyping, 610 dogs were genotyped (Greyhounds within the pedigree n= 80; dogs of various breeds without PRA n= 530). Only the affected dogs (males n= 39; female n=1) had the deletion.

Conclusions : Variants in CACNA1F cause multiple retinal disorders such as congenital stationary night blindness type 2A, cone-rod dystrophy and Åland Island eye disease in humans. We identified a novel deletion in CACNA1F in racing Greyhounds. This is the first large animal disease model for CACNA1F-related ocular disease and could be used to test novel therapies for humans.

This abstract was presented at the 2024 ARVO Annual Meeting, held in Seattle, WA, May 5-9, 2024.