A Deep Intronic PKHD1 Variant Identified by SpliceAI in a Deceased Neonate With Autosomal Recessive Polycystic Kidney Disease

Felix Richter, Kayleigh D. Rutherford, Anisha J. Cooke, Malorie Meshkati, Vanessa Eddy-Abrams, Daniel Greene, Jordana Kosowsky, Yeaji Park, Surabhi Aggarwal, Rebecca J. Burke, Weili Chang, Jillian Connors, Peter J. Giannone, Thomas Hays, Divya Khattar, Mark Polak, Liana Senaldi, Matthew Smith-Raska, Shanthy Sridhar, Laurie SteinerJonathan R. Swanson, Kate A. Tauber, Mafalda Barbosa, Katherine F. Guttmann, Ernest Turro

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

The etiologies of newborn deaths in neonatal intensive care units usually remain unknown, even after genetic testing. Whole-genome sequencing, combined with artificial intelligence–based methods for predicting the effects of non-coding variants, provide an avenue for resolving these deaths. Using one such method, SpliceAI, we identified a maternally inherited deep intronic PKHD1 splice variant (chr6:52030169T>C), in trans with a pathogenic missense variant (p.Thr36Met), in a newborn who died of autosomal recessive polycystic kidney disease at age 2 days. We validated the deep intronic variant's impact in maternal urine–derived cells expressing PKHD1. Reverse transcription polymerase chain reaction followed by Sanger sequencing showed that the variant causes inclusion of 147 bp of the canonical intron between exons 29 and 30 of PKHD1 into the mRNA, including a premature stop codon. Allele-specific expression analysis at a heterozygous site in the mother showed that the mutant allele completely suppresses canonical splicing. In an unrelated healthy control, there was no evidence of transcripts including the novel splice junction. We returned a diagnostic report to the parents, who underwent in vitro embryo selection.

Original languageEnglish
Pages (from-to)829-833
Number of pages5
JournalAmerican Journal of Kidney Diseases
Volume83
Issue number6
DOIs
StatePublished - Jun 2024

Bibliographical note

Publisher Copyright:
© 2024 National Kidney Foundation, Inc.

Funding

Felix Richter, MD, PhD, Kayleigh D. Rutherford, MS, Anisha J. Cooke, MS, Malorie Meshkati, MD, Vanessa Eddy-Abrams, MD, Daniel Greene, PhD, Jordana Kosowsky, MS, Yeaji Park, BA, Surabhi Aggarwal, MD, Rebecca J. Burke, MD, PhD, Weili Chang, MD, Jillian Connors, MD, Peter J. Giannone, MD, Thomas Hays, MD, Divya Khattar, MD, Mark Polak, MD, Liana Senaldi, MD, Matthew Smith-Raska, MD, PhD, Shanthy Sridhar, MD, Laurie Steiner, MD, Jonathan R. Swanson, MD, Kate A. Tauber, MD, Mafalda Barbosa, MD, Katherine F. Guttmann, MD, and Ernest Turro, PhD. FR, KDR, and AJC contributed equally to this work. This work was supported by a Mindich Child Health and Development pilot award. This work used resources provided by Scientific Computing at the Icahn School of Medicine at Mount Sinai, which is supported by grant UL1TR004419 from the National Center for Advancing Translational Sciences and grants S10OD026880 and S10OD030463 from the National Institutes of Health. Dr Turro is supported by the Lowy Foundation USA and by NIH awards R01HL161365 and R03HD111492. The funders did not have a role in defining the content of the manuscript. The authors declare that they have no relevant financial interests. We thank the parents for graciously enrolling in the NICUnet study and being willing partners in identifying the cause of their son's death. We are grateful to Molly Arnn for assisting with NICUnet study logistics. We thank Jane Houldsworth, Aneta Waluszko, and William Lam from the Mount Sinai Molecular Pathology laboratory for CLIA-certified DNA extraction and DNA storage. We thank Lisa Satlin and Talia Swartz from Mount Sinai for providing culture media components and Rebecca Dewhurst and John Sayer from Newcastle University for their advice on urine-derived renal epithelial cell experiments. We acknowledge the support of Laura Andolina, Mark Polizzi, Alicia Braxton, and Nora Alexander at GeneDx. We thank all the members and support staff of the NICUnet study collaboration network. The authors declare that they have obtained written consent, from a relative with appropriate authority, for publication of the information about the patient that appears within this Case Report and any associated supplementary material. Received July 31, 2023. Evaluated by 2 external peer reviewers and a radiologist, with direct editorial input from an Associate Editor and a Deputy Editor. Accepted in revised form November 10, 2023. Support : This work was supported by a Mindich Child Health and Development pilot award. This work used resources provided by Scientific Computing at the Icahn School of Medicine at Mount Sinai, which is supported by grant UL1TR004419 from the National Center for Advancing Translational Sciences and grants S10OD026880 and S10OD030463 from the National Institutes of Health. E.T. is supported by the Lowy Foundation USA and by NIH awards R01HL161365 and R03HD111492. The funders did not have a role in defining the content of the manuscript.

FundersFunder number
Lowy Foundation
Mindich Child Health and Development
Nora Alexander at GeneDx
National Institutes of Health (NIH)R01HL161365, R03HD111492
National Institutes of Health (NIH)
National Center for Advancing Translational Sciences (NCATS)S10OD030463, S10OD026880
National Center for Advancing Translational Sciences (NCATS)
Icahn School of Medicine at Mount SinaiUL1TR004419
Icahn School of Medicine at Mount Sinai
Newcastle University

    Keywords

    • ARPKD
    • Deceased
    • Intronic
    • NICU
    • PKHD1
    • SpliceAI

    ASJC Scopus subject areas

    • Nephrology

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