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Get Free AccessIncomplete penetrance, or absence of disease phenotype in an individual with a disease-associated variant, is a major challenge in variant interpretation. Studying individuals with apparent incomplete penetrance can shed light on underlying drivers of altered phenotype penetrance. Here, we investigate clinically relevant variants from ClinVar in 807,162 individuals from the Genome Aggregation Database (gnomAD), demonstrating improved representation in gnomAD version 4. We then conduct a comprehensive case-by-case assessment of 734 predicted loss of function variants in 77 genes associated with severe, early-onset, highly penetrant haploinsufficient disease. Here, we identify explanations for the presumed lack of disease manifestation in 701 of 734 variants (95%). Individuals with unexplained lack of disease manifestation in this set of disorders are rare, underscoring the need and power of deep case-by-case assessment presented here to minimize false assignments of disease risk, particularly in unaffected individuals with higher rates of secondary properties that result in rescue.
Fernando S. Goes, Sanna Gudmundsson, Moriel Singer‐Berk, Sarah L. Stenton, Julia K. Goodrich, Michael W. Wilson, Jonah Einson, Nicholas A. Watts, María T. Abreu, Amina Abubakar, Rolf Adolfsson, Carlos A. Aguilar‐Salinas, Tariq Ahmad, Christine M. Albert, Jessica Alföldi, Matthieu Allez, Celso Arango, Diego Ardissino, Irina M. Armean, Elizabeth G. Atkinson, Gil Atzmon, Eric Banks, J. A. Barnard, Samantha Baxter, Laurent Beaugerie, David Benjamin, Emelia Benjamin, Louis Bergelson, Çharles N. Bernstein, Douglas Blackwood, Michael Boehnke, Lori L. Bonnycastle, Erwin P. Böttinger, Donald W. Bowden, Matthew J. Bown, Harrison Brand, Steven R. Brant, Ted Brookings, Sam Bryant, Shawneequa Callier, Hannia Campos, John C. Chambers, Juliana C.N. Chan, Katherine R. Chao, Sinéad B. Chapman, Daniel I. Chasman, Lea Ann Chen, Siwei Chen, Rex L. Chisholm, Judy H. Cho, Rajiv Chowdhury, Mina K. Chung, Wendy K. Chung, Kristian Cibulskis, Bruce M. Cohen, Ryan L. Collins, Kristen M. Connolly, Adolfo Correa, Aiden Corvin, Miguel Covarrubias, Nick Craddock, Beryl B. Cummings, Dana Dabelea, John Danesh, Dawood Darbar, Phil Darnowsky, Joshua C. Denny, Stacey Donnelly, Richard H. Duerr, Ravindranath Duggirala, Josée Dupuis, Patrick T. Ellinor, Roberto Elosúa, James Emery, Eleina England, Jeanette Erdmann, Tõnu Esko, Emily Evangelista, Yossi Farjoun, Diane Fatkin, William A. Faubion, Steven Ferriera, Gemma A. Figtree, Kelly Flannagan, José C. Florez, Laurent C. Francioli, André Franke, Adam Frankish, Jack Fu, Martti Färkkilâ, Stacey Gabriel, Kiran Garimella, Laura D. Gauthier, Jeff Gentry, Michel Georges, Gad Getz, David C. Glahn, Benjamin Gläser, René S. Kahn (2025). Exploring penetrance of clinically relevant variants in over 800,000 humans from the Genome Aggregation Database. , 16(1), DOI: https://doi.org/10.1038/s41467-025-61698-x.
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Type
Article
Year
2025
Authors
99
Datasets
0
Total Files
0
Language
en
DOI
https://doi.org/10.1038/s41467-025-61698-x
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