A nonsense variant in Rap Guanine Nucleotide Exchange Factor 5 (RAPGEF5) is associated with equine familial isolated hypoparathyroidism in Thoroughbred Foals.

Author summary The Thoroughbred breeding industry in the United States produces a total impact of $6 billion. A lethal hypocalcemic syndrome was first described in young Thoroughbred horses in 1997. Affected foals suffer from seizures due to low blood calcium concentrations in the first few weeks of life. Our clinical evaluation of affected foals supported a diagnosis of primary hypoparathyroidism and the disease appeared to be inherited as an autosomal recessive trait. Whole-genome sequencing of two affected foals identified a nonsense variant inRAPGEF5. Two additional affected foals were subsequently genotyped and also homozygous for the nonsense variant. Overexpression of the equine variant in frog embryos demonstrated loss-of-function. Genetic testing is now available to screen carrier Thoroughbreds and the disease was renamed equine isolated familial hypoparathyroidism (EIFH). Idiopathic hypocalcemia in Thoroughbred (TB) foals causes tetany and seizures and is invariably fatal. Based upon the similarity of this disease with human familial hypoparathyroidism and occurrence only in the TB breed, we conducted a genetic investigation on two affected TB foals. Familial hypoparathyroidism was identified, and pedigree analysis suggested an autosomal recessive (AR) mode of inheritance. We performed whole-genome sequencing of the two foals, their unaffected dams and four unaffected, unrelated TB horses. Both homozygosity mapping and an association analysis were used to prioritize potential genetic variants. Of the 2,808 variants that significantly associated with the phenotype using an AR mode of inheritance (P<0.02) and located within a region of homozygosity, 1,507 (54%) were located in a 9.7 Mb region on chr4 (44.9-54.6 Mb). Within this region, a nonsense variant (RAPGEF5c.2624C>A,p.Ser875*) was significantly associated with the hypoparathyroid phenotype (P-allelic= 0.008). Affected foals were homozygous for the variant, with two additional affected foals subsequently confirmed in 2019. Necropsies of all affected foals failed to identify any histologically normal parathyroid glands. Because the nonsense mutation inRAPGEF5was near the C-terminal end of the protein, the impact on protein function was unclear. Therefore, we tested the variant in our Xenopus overexpression model and demonstrated RAPGEF5 loss-of-function. ThisRAPGEF5variant represents the first genetic variant for hypoparathyroidism identified in any domestic animal species.