Integrated in silico and experimental assessment of disease relevance of PCDH19 missense variants

Duyen H Pham; Melissa R Pitman; Raman Kumar; Lachlan A Jolly; Renee Schulz; Alison E Gardner; Rebekah de Nys; Sarah E Heron; Mark A Corbett; Kavitha Kothur; Deepak Gill; Sulekha Rajagopalan; Kristy L Kolc; Benjamin J Halliday; Stephen P Robertson; Brigid M Regan; Heidi E Kirsch; Samuel F Berkovic; Ingrid E Scheffer; Stuart M Pitson; Slave Petrovski; Jozef Gecz

doi:10.1002/humu.24237

Integrated in silico and experimental assessment of disease relevance of PCDH19 missense variants

Hum Mutat. 2021 Aug;42(8):1030-1041. doi: 10.1002/humu.24237. Epub 2021 Jun 15.

Authors

Duyen H Pham^{1

2}, Melissa R Pitman³, Raman Kumar^{1

2}, Lachlan A Jolly^{1

2}, Renee Schulz¹, Alison E Gardner^{1

2}, Rebekah de Nys^{1

2}, Sarah E Heron^{1

2}, Mark A Corbett^{1

2}, Kavitha Kothur^{4

5}, Deepak Gill^{4

5}, Sulekha Rajagopalan⁶, Kristy L Kolc^{1

2}, Benjamin J Halliday⁷, Stephen P Robertson⁷, Brigid M Regan⁸, Heidi E Kirsch⁹, Samuel F Berkovic⁸, Ingrid E Scheffer^{8

10

11}, Stuart M Pitson^{1

3

12}, Slave Petrovski^{13

14}, Jozef Gecz^{1

2

12

15}

Affiliations

¹ Neurogenetics, Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia.
² Paediatrics and Reproductive Health, Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia.
³ Molecular Therapeutics, Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia.
⁴ Department of Paediatrics and Child Health, Kids Neuroscience Centre, The University of Sydney, Sydney, New South Wales, Australia.
⁵ TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Sydney, New South Wales, Australia.
⁶ Department of Clinical Genetics, Liverpool Hospital, Liverpool, New South Wales, Australia.
⁷ Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.
⁸ Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, Victoria, Australia.
⁹ Department of Neurology, University of California, San Francisco, California, USA.
¹⁰ Department of Paediatrics, Royal Children's Hospital, University of Melbourne, Flemington, Victoria, Australia.
¹¹ Epilepsy Research Centre, Florey Institute of Neuroscience and Mental Health, Heidelberg, Victoria, Australia.
¹² School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia.
¹³ Centre for Genomics Research, Precision Medicine and Genomics, IMED Biotech Unit, AstraZeneca, Cambridge, UK.
¹⁴ Department of Medicine, University of Melbourne, Parkville, Victoria, Australia.
¹⁵ Women and Kids, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.

PMID: 34082468
DOI: 10.1002/humu.24237

Abstract

PCDH19 is a nonclustered protocadherin molecule involved in axon bundling, synapse function, and transcriptional coregulation. Pathogenic variants in PCDH19 cause infantile-onset epilepsy known as PCDH19-clustering epilepsy or PCDH19-CE. Recent advances in DNA-sequencing technologies have led to a significant increase in the number of reported PCDH19-CE variants, many of uncertain significance. We aimed to determine the best approaches for assessing the disease relevance of missense variants in PCDH19. The application of the American College of Medical Genetics and Association for Molecular Pathology (ACMG-AMP) guidelines was only 50% accurate. Using a training set of 322 known benign or pathogenic missense variants, we identified MutPred2, MutationAssessor, and GPP as the best performing in silico tools. We generated a protein structural model of the extracellular domain and assessed 24 missense variants. We also assessed 24 variants using an in vitro reporter assay. A combination of these tools was 93% accurate in assessing known pathogenic and benign PCDH19 variants. We increased the accuracy of the ACMG-AMP classification of 45 PCDH19 variants from 50% to 94%, using these tools. In summary, we have developed a robust toolbox for the assessment of PCDH19 variant pathogenicity to improve the accuracy of PCDH19-CE variant classification.

Keywords: PCDH19; VUS; epilepsy; functional test; variant assessment.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cadherins* / genetics
Epilepsy*
Humans
Mutation, Missense
Protocadherins
Sequence Analysis, DNA

Substances

Cadherins
PCDH19 protein, human
Protocadherins