The functional impact of 1,570 individual amino acid substitutions in human OTC

Russell S. Lo, Pacific Northwest Research Institute, Seattle, WA, USA.
Gareth A. Cromie, Pacific Northwest Research Institute, Seattle, WA, USA.
Michelle Tang, Pacific Northwest Research Institute, Seattle, WA, USA.
Kevin Teng, Pacific Northwest Research Institute, Seattle, WA, USA.
Katherine Owens, Pacific Northwest Research Institute, Seattle, WA, USA; Department of Applied Mathematics, University of Washington, Seattle, WA, USA.
Amy Sirr, Pacific Northwest Research Institute, Seattle, WA, USA.
J Nathan Kutz, Department of Applied Mathematics, University of Washington, Seattle, WA, USA.
Hiroki Morizono, Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA.
Ljubica Caldovic, Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA.
Nicholas Ah Mew, Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA.
Andrea Gropman, Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA; Department of Neurology, Division of Neurogenetics and Neurodevelopmental Disabilities, Children's National Hospital, Washington, DC, USA; Center for Neuroscience Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA.
Aimée M. Dudley, Pacific Northwest Research Institute, Seattle, WA, USA. Electronic address: aimee.dudley@gmail.com.

Document Type

Journal Article

Publication Date

5-4-2023

Journal

American journal of human genetics

Volume

110

Issue

5

DOI

10.1016/j.ajhg.2023.03.019

Keywords

OTC deficiency; Oxford Nanopore sequencing; SNV analysis/discovery; X-linked disease; metabolic disorder; model organisms; multiplexed assays of variant effect; rare disease; rare variants; urea cycle disorder; variant interpretation

Abstract

Deleterious mutations in the X-linked gene encoding ornithine transcarbamylase (OTC) cause the most common urea cycle disorder, OTC deficiency. This rare but highly actionable disease can present with severe neonatal onset in males or with later onset in either sex. Individuals with neonatal onset appear normal at birth but rapidly develop hyperammonemia, which can progress to cerebral edema, coma, and death, outcomes ameliorated by rapid diagnosis and treatment. Here, we develop a high-throughput functional assay for human OTC and individually measure the impact of 1,570 variants, 84% of all SNV-accessible missense mutations. Comparison to existing clinical significance calls, demonstrated that our assay distinguishes known benign from pathogenic variants and variants with neonatal onset from late-onset disease presentation. This functional stratification allowed us to identify score ranges corresponding to clinically relevant levels of impairment of OTC activity. Examining the results of our assay in the context of protein structure further allowed us to identify a 13 amino acid domain, the SMG loop, whose function appears to be required in human cells but not in yeast. Finally, inclusion of our data as PS3 evidence under the current ACMG guidelines, in a pilot reclassification of 34 variants with complete loss of activity, would change the classification of 22 from variants of unknown significance to clinically actionable likely pathogenic variants. These results illustrate how large-scale functional assays are especially powerful when applied to rare genetic diseases.

Department

Neurology

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