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Get Free AccessAbstract Upstream open reading frames (uORFs) are important tissue-specific cis -regulators of protein translation. Although isolated case reports have shown that variants that create or disrupt uORFs can cause disease, genetic sequencing approaches typically focus on protein-coding regions and ignore these variants. Here, we describe a systematic genome-wide study of variants that create and disrupt human uORFs, and explore their role in human disease using 15,708 whole genome sequences collected by the Genome Aggregation Database (gnomAD) project. We show that 14,897 variants that create new start codons upstream of the canonical coding sequence (CDS), and 2,406 variants disrupting the stop site of existing uORFs, are under strong negative selection. Furthermore, variants creating uORFs that overlap the CDS show signals of selection equivalent to coding loss-of-function variants, and uORF-perturbing variants are under strong selection when arising upstream of known disease genes and genes intolerant to loss-of-function variants. Finally, we identify specific genes where perturbation of uORFs is likely to represent an important disease mechanism, and report a novel uORF frameshift variant upstream of NF2 in families with neurofibromatosis. Our results highlight uORF-perturbing variants as an important and under-recognised functional class that can contribute to penetrant human disease, and demonstrate the power of large-scale population sequencing data to study the deleteriousness of specific classes of non-coding variants.
Nicola Whiffin, Konrad J. Karczewski, Xiaolei Zhang, Sonia Chothani, Miriam J. Smith, D. Gareth Evans, Angharad M. Roberts, Nicholas M. Quaife, Sebastian Schäfer, Owen J. L. Rackham, Anne O’Donnell‐Luria, Laurent C. Francioli, Irina M. Armean, Eric Banks, Louis Bergelson, Kristian Cibulskis, Ryan L. Collins, Kristen M. Connolly, Miguel Covarrubias, Beryl B. Cummings, Stacey Donnelly, Yossi Farjoun, Steven Ferriera, Laurent C. Francioli, Stacey Gabriel, Laura D. Gauthier, Jeff Gentry, Namrata Gupta, Thibault Jeandet, Diane Kaplan, Konrad J. Karczewski, Kristen M. Laricchia, Christopher Llanwarne, Eric Vallabh Minikel, 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, Qingbo S. Wang, James S. Ware, Nicholas A. Watts, Ben Weisburd, Nicola Whiffin, 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, Tõnu Esko, Martti Färkkilâ, José C. Florez, André Franke, Gad Getz, Benjamin Gläser, Stephen J. Glatt, David Goldstein, Clicerio González (2019). Characterising the loss-of-function impact of 5’ untranslated region variants in whole genome sequence data from 15,708 individuals. , DOI: https://doi.org/10.1101/543504.
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Type
Preprint
Year
2019
Authors
95
Datasets
0
Total Files
0
Language
en
DOI
https://doi.org/10.1101/543504
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