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PLoS genetics2020; 16(9); e1009028; doi: 10.1371/journal.pgen.1009028

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

Abstract: 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 (RAPGEF5 c.2624C>A,p.Ser875*) was significantly associated with the hypoparathyroid phenotype (Pallelic = 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 in RAPGEF5 was 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. This RAPGEF5 variant represents the first genetic variant for hypoparathyroidism identified in any domestic animal species.
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Publication Date: 2020-09-28 PubMed ID: 32986719PubMed Central: PMC7544121DOI: 10.1371/journal.pgen.1009028Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The article presents research identifying a specific genetic variant in the RAPGEF5 gene related to hypoparathyroidism, a fatal condition in Thoroughbred foals. The study uses whole genome sequencing, pedigree analysis and tests the impact of this mutation in the Xenopus overexpression model.

Background

  • The study largely focuses on addressing Idiopathic hypocalcemia in Thoroughbred (TB) foals. This is a typically fatal condition that results in seizures and tetany in the affected foals.
  • In order to understand the genetic basis of this disease, the research team compared it to human familial hypoparathyroidism given the similar effects and investigated two affected foals belonging to the TB breed.

Genetic Analysis and Findings

  • The team performed in-depth genetic studies by conducting a pedigree analysis and whole-genome sequencing of not just the affected foals, but also their healthy mothers and four unrelated TB horses who were normal.
  • The pedigree analysis suggested that the disease follows an autosomal recessive mode of inheritance, meaning that the offspring must inherit a copy of the defective gene from both parents to develop the disease.
  • Through the process of homozygosity mapping and conducting association analysis, the researchers identified that 54% of significant variants were located in a particular region on chr4.
  • Upon further scrutiny, the researchers found a specific nonsense genetic variant (c.2624C>A,p.Ser875*) in the Rap Guanine Nucleotide Exchange Factor 5 (RAPGEF5) was highly associated with the hypoparathyroid phenotype.

Validation and Impact of Mutation

  • The affected foals were homozygous for this variant, i.e., they possessed two copies of the defect RAPGEF5 gene – one from each parent.
  • This observation was further confirmed with two more foals that were found to be affected in 2019.
  • An examination of the necropsy results revealed there were no histologically normal parathyroid glands in any of the affected foals, pointing towards the detrimental impact of the variant.
  • Considering the complexity of the mutation, which was found near the C-terminal end of the protein, the researchers utilized the Xenopus overexpression model to understand the effects of the variant.
  • The model demonstrated a loss-of-function in the RAPGEF5 gene due to the mutation, confirming its role in the disease.

Conclusion

  • The nonsense variant in the RAPGEF5 gene identified through this study is the first genetic variant for hypoparathyroidism identified in any domestic animal species.
  • This discovery could prove instrumental in developing treatments, preventive measures, and improving understanding of hypoparathyroidism in veterinary science.

Cite This Article

APA
Rivas VN, Magdesian KG, Fagan S, Slovis NM, Luethy D, Javsicas LH, Caserto BG, Miller AD, Dahlgren AR, Peterson J, Hales EN, Peng S, Watson KD, Khokha MK, Finno CJ. (2020). A nonsense variant in Rap Guanine Nucleotide Exchange Factor 5 (RAPGEF5) is associated with equine familial isolated hypoparathyroidism in Thoroughbred foals. PLoS Genet, 16(9), e1009028. https://doi.org/10.1371/journal.pgen.1009028

Publication

PLoS genetics
ISSN: 1553-7404
NlmUniqueID: 101239074
Country: United States
Language: English
Volume: 16
Issue: 9
Pages: e1009028

Researcher Affiliations

Rivas, Victor N
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America.
Magdesian, K Gary
  • Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America.
Fagan, Sophia
  • Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale School of Medicine, Yale University, New Haven, Connecticut, United States of America.
Slovis, Nathan M
  • Hagyard Equine Medical Hospital, Lexington, Kentucky, United States of America.
Luethy, Daniela
  • Department of Clinical Studies-New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
Javsicas, Laura H
  • Rhinebeck Equine L.L.P., Rhinebeck, New York, United States of America.
Caserto, Brian G
  • VetPath Services, Stone Ridge, NY, United States of America.
Miller, Andrew D
  • Department of Biomedical Sciences, Section of Anatomic Pathology, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America.
Dahlgren, Anna R
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America.
Peterson, Janel
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America.
Hales, Erin N
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America.
Peng, Sichong
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America.
Watson, Katherine D
  • Department of Anatomic Pathology, Veterinary Medical Teaching Hospital, University of California-Davis, Davis, California, United States of America.
Khokha, Mustafa K
  • Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale School of Medicine, Yale University, New Haven, Connecticut, United States of America.
Finno, Carrie J
  • Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, California, United States of America.

MeSH Terms

  • Animals
  • Codon, Nonsense
  • Embryo, Nonmammalian
  • Female
  • Homozygote
  • Horse Diseases / etiology
  • Horse Diseases / genetics
  • Horses
  • Hypocalcemia / genetics
  • Hypocalcemia / pathology
  • Hypocalcemia / veterinary
  • Hypoparathyroidism / genetics
  • Hypoparathyroidism / pathology
  • Hypoparathyroidism / veterinary
  • Male
  • Pedigree
  • Whole Genome Sequencing
  • Xenopus / embryology
  • ras Guanine Nucleotide Exchange Factors / chemistry
  • ras Guanine Nucleotide Exchange Factors / genetics
  • ras Guanine Nucleotide Exchange Factors / metabolism

Grant Funding

  • L40 TR001136 / NCATS NIH HHS
  • UL1 TR001863 / NCATS NIH HHS
  • R01 HD081379 / NICHD NIH HHS
  • R01 HD102186 / NICHD NIH HHS
  • K01 OD015134 / NIH HHS

Conflict of Interest Statement

The authors have declared that no competing interests exist.

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Citations

This article has been cited 3 times.
  1. Butylina M, Föger-Samwald U, Gelles K, Pietschmann P, Sipos W. Challenges in establishing animal models for studying osteoimmunology of hypoparathyroidism. Front Vet Sci 2023;10:1163903.
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  2. Elcombe ME, Bellone RR, Magdesian KG, Finno CJ. Prevalence of the RAPGEF5 c.2624C>A and PLOD1 c.2032G>A variants associated with equine familial isolated hypoparathyroidism and fragile foal syndrome in the US Thoroughbred population (1988-2019). Equine Vet J 2023 Jul;55(4):666-671.
    doi: 10.1111/evj.13883pubmed: 36199159google scholar: lookup
  3. Peng S, Petersen JL, Bellone RR, Kalbfleisch T, Kingsley NB, Barber AM, Cappelletti E, Giulotto E, Finno CJ. Decoding the Equine Genome: Lessons from ENCODE. Genes (Basel) 2021 Oct 27;12(11).
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