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  5. The effect of LRRK2 loss-of-function variants in humans

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Article
en
2020

The effect of LRRK2 loss-of-function variants in humans

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en
2020
Vol 26 (6)
Vol. 26
DOI: 10.1038/s41591-020-0893-5

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Emelia Benjamin
Emelia Benjamin

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Nicola Whiffin
Irina M. Armean
Aaron Kleinman
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Abstract

Human genetic variants predicted to cause loss-of-function of protein-coding genes (pLoF variants) provide natural in vivo models of human gene inactivation and can be valuable indicators of gene function and the potential toxicity of therapeutic inhibitors targeting these genes1,2. Gain-of-kinase-function variants in LRRK2 are known to significantly increase the risk of Parkinson's disease3,4, suggesting that inhibition of LRRK2 kinase activity is a promising therapeutic strategy. While preclinical studies in model organisms have raised some on-target toxicity concerns5-8, the biological consequences of LRRK2 inhibition have not been well characterized in humans. Here, we systematically analyze pLoF variants in LRRK2 observed across 141,456 individuals sequenced in the Genome Aggregation Database (gnomAD)9, 49,960 exome-sequenced individuals from the UK Biobank and over 4 million participants in the 23andMe genotyped dataset. After stringent variant curation, we identify 1,455 individuals with high-confidence pLoF variants in LRRK2. Experimental validation of three variants, combined with previous work10, confirmed reduced protein levels in 82.5% of our cohort. We show that heterozygous pLoF variants in LRRK2 reduce LRRK2 protein levels but that these are not strongly associated with any specific phenotype or disease state. Our results demonstrate the value of large-scale genomic databases and phenotyping of human loss-of-function carriers for target validation in drug discovery.

How to cite this publication

Nicola Whiffin, Irina M. Armean, Aaron Kleinman, Jamie L. Marshall, Eric Vallabh Minikel, Julia K. Goodrich, Nicholas M. Quaife, Joanne B. Cole, Qingbo S. Wang, Konrad J. Karczewski, Beryl B. Cummings, Laurent C. Francioli, Kristen M. Laricchia, Anna Guan, Babak Alipanahi, Peter Morrison, Marco A. S. Baptista, Juliana C.N. Chan, Irina M. Armean, Eric Banks, Louis Bergelson, Kristian Cibulskis, Ryan L. Collins, Kristen M. Connolly, Miguel Covarrubias, Beryl B. Cummings, Mark J. Daly, Stacey Donnelly, Yossi Farjoun, Steven Ferriera, Stacey Gabriel, Laura D. Gauthier, Jeff Gentry, Namrata Gupta, Thibault Jeandet, Diane Kaplan, Kristen M. Laricchia, Christopher Llanwarne, Ruchi Munshi, Benjamin M. Neale, Sam Novod, Anne O’Donnell‐Luria, Nikelle Petrillo, Timothy Poterba, David Roazen, Valentín Ruano-Rubio, Andrea Saltzman, Kaitlin E. Samocha, Molly Schleicher, Cotton Seed, Matthew Solomonson, José Soto, Grace Tiao, Kathleen Tibbetts, Charlotte Tolonen, Christopher Vittal, Gordon Wade, Arcturus Wang, Nicholas A. Watts, Ben Weisburd, Carlos A. Aguilar‐Salinas, Tariq Ahmad, Christine M. Albert, Diego Ardissino, Gil Atzmon, John Barnard, Laurent Beaugerie, Emelia Benjamin, Michael Boehnke, Lori L. Bonnycastle, Erwin P. Böttinger, Donald W. Bowden, Matthew J. Bown, John C. Chambers, Juliana C.N. Chan, Daniel I. Chasman, Judy H. Cho, Mina K. Chung, Bruce M. Cohen, Adolfo Correa, Dana Dabelea, Dawood Darbar, Ravindranath Duggirala, Josée Dupuis, Patrick T. Ellinor, Roberto Elosúa, Jeanette Erdmann, Martti Färkkilâ, José C. Florez, André Franke, Gad Getz, Benjamin Gläser, Stephen J. Glatt, David Goldstein, Clicerio González, Leif Groop, Christopher Haiman, Craig L. Hanis, Matthew B. Harms (2020). The effect of LRRK2 loss-of-function variants in humans. , 26(6), DOI: https://doi.org/10.1038/s41591-020-0893-5.

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Publication Details

Type

Article

Year

2020

Authors

99

Datasets

0

Total Files

0

Language

en

DOI

https://doi.org/10.1038/s41591-020-0893-5

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