Exploring penetrance of clinically relevant variants in over 800,000 humans from the Genome Aggregation Database
Abstract
Abstract Incomplete 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.
Article Details
Authors (306)
Moriel Singer-Berk
Sarah L. Stenton
Julia K. Goodrich
Michael W. Wilson
Jonah Einson
Maria Abreu
Amina Abubakar
Rolf Adolfsson
Carlos A. Aguilar Salinas
Tariq Ahmad
Christine M. Albert
Department of Cardiology, Smidt Heart Institute, Cedars–Sinai Medical Center, Los Angeles
Jessica Alföldi
Matthieu Allez
Celso Arango López
Diego Ardissino
Irina M. Armean
Elizabeth G. Atkinson
Gil Atzmon
Eric Banks
John Barnard
Samantha M. Baxter
Laurent Beaugerie
David Benjamin
Emelia J. Benjamin
Louis Bergelson
Charles Bernstein
Douglas Blackwood
Michael Boehnke
Lori L. Bonnycastle
Erwin P. Bottinger
Donald W. Bowden
Matthew J. Bown
Harrison Brand
Steven Brant
Ted Brookings
Sam Bryant
Shawneequa L. Callier
Hannia Campos
John C. Chambers
Juliana C. Chan
Katherine R. Chao
Sinéad Chapman
Daniel I. Chasman
Lea A. Chen
Siwei Chen
Rex Chisholm
Judy Cho
Rajiv Chowdhury
Mina K. Chung
Wendy K. Chung
Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School
Kristian Cibulskis
Bruce Cohen
Ryan L. Collins
Kristen M. Connolly
Adolfo Correa
Aiden Corvin
Miguel Covarrubias
Nick Craddock
Beryl B. Cummings
Dana Dabelea
Mark J. Daly
John Danesh
Dawood Darbar
Phil Darnowsky
Joshua C. Denny
Stacey Donnelly
Richard H. Duerr
Ravindranath Duggirala
Josée Dupuis
Patrick T. Ellinor
Roberto Elosua
James Emery
Eleina England
Jeanette Erdmann
Tõnu Esko
Emily Evangelista
Yossi Farjoun
Diane Fatkin
William Faubion
Steven Ferriera
Gemma Figtree
Kelly Flannagan
Jose Florez
Laurent Francioli
Andre Franke
Adam Frankish
Jack Fu
Martti Färkkilä
Stacey Gabriel
Kiran Garimella
Laura D. Gauthier
Jeff Gentry
Michel Georges
Gad Getz
David C. Glahn
Benjamin Glaser
Stephen J. Glatt
Fernando S. Goes
David Goldstein
Clicerio Gonzalez
Julia Goodrich
Riley H. Grant
Leif Groop
Sanna Gudmundsson
Namrata Gupta
Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Andrea Haessly
Christopher Haiman
Ira Hall
Craig L. Hanis
James Hanyok
Matthew Harms
Qin He
State Key Laboratory of Soil Pollution Control and Safety, Department of Chemistry
Mikko Hiltunen
Matti M. Holi
Christina M. Hultman
Steve Jahl
Chaim Jalas
Thibault Jeandet
Mikko Kallela
Diane Kaplan
Jaakko Kaprio
Konrad J. Karczewski
Elizabeth W. Karlson
Sekar Kathiresan
Verve Therapeutics, a wholly owned subsidiary of Eli Lilly, Boston
Eimear E. Kenny
Bong-Jo Kim
Young Jin Kim
Daniel King
George Kirov
Zan Koenig
Jaspal Kooner
Seppo Koskinen
Harlan M. Krumholz
Subra Kugathasan
Juozas Kupcinskas
Soo Heon Kwak
Markku Laakso
Nicole Lake
Mikael Landén
Trevyn Langsford
Kristen M. Laricchia
Terho Lehtimäki
Monkol Lek
Department of Genetics, Yale School of Medicine
James Lewis
Cecilia M. Lindgren
Emily Lipscomb
Christopher Llanwarne
Ruth J. F. Loos
Edouard Louis
Chelsea Lowther
Wenhan Lu
Steven A. Lubitz
Tom Lyons
Ronald C. W. Ma
Dara S. Manoach
Gregory M. Marcus
Division of Cardiology, University of California, San Francisco, San Francisco
Jaume Marrugat
Nicholas Marston
Daniel M. Marten
Alicia R. Martin
Kari M. Mattila
Steven McCarroll
Mark I. McCarthy
Jacob L. McCauley
Dermot McGovern
Ruth McPherson
Andrew MacQuillin
James B. Meigs
Olle Melander
Andres Metspalu
Deborah Meyers
Eric V. Minikel
Braxton D. Mitchell
Paul Moayyedi
Farncombe Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
Sanghamitra Mohanty
Andrés Moreno Estrada
Nicola J. Mulder
Ruchi Munshi
Aliya Naheed
Andrea Natale
Texas Cardiac Arrhythmia Research, St. David’s Medical Center, Austin
Saman Nazarian
Benjamin M. Neale
Charles Newton
Peter M. Nilsson
Sam Novod
Anne H. O’Donnell-Luria
Michael C. O’Donovan
Yukinori Okada
Dost Ongur
Roel Ophoff
Lorena Orozco
Willem Ouwehand
Michael J. Owen
Nick Owen
Colin Palmer
Nicholette D. Palmer
Aarno Palotie
Mara Parellada
Kyong Soo Park
Carlos Pato
Nancy L. Pedersen
Tina Pesaran
Nikelle Petrillo
William Phu
Sharon Plon
Danielle Posthuma
Timothy Poterba
Ann E. Pulver
Aaron Quinlan
Dan Rader
Nazneen Rahman
Heidi Rehm
Andreas Reif
Alex Reiner
Department of Epidemiology, University of Washington, Seattle, WA, USA.
Anne M. Remes
Dan Rhodes
Stephen Rich
John D. Rioux
Samuli Ripatti
David Roazen
Jason Roberts
Elise Robinson
Molecular Imaging Program at Stanford, Department of Radiology, School of Medicine, Stanford University
Dan M. Roden
Jerome I. Rotter
Guy Rouleau
Valentin Ruano-Rubio
Christian T. Ruff
Heiko Runz
Marc S. Sabatine
TIMI Study Group, Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston
Nareh Sahakian
Danish Saleheen
Veikko Salomaa
Andrea Saltzman
Nilesh J. Samani
Kaitlin E. Samocha
Alba Sanchis-Juan
Akira Sawa
Jeremiah Scharf
Molly Schleicher
Patrick Schultz
Heribert Schunkert
DZHK Partner Site Munich, Munich Heart Alliance, Munich, Germany
Sebastian Schönherr
Eleanor G. Seaby
Cotton Seed
Svati H. Shah
Megan Shand
Ted Sharpe
Moore B. Shoemaker
Tai Shyong
Edwin K. Silverman
Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA.
Jurgita Skiecevičienė
Pamela Sklar
J. Gustav Smith
Jonathan T. Smith
Jordan Smoller
Hilkka Soininen
Harry Sokol
Matthew Solomonson
Rachel G. Son
Jose Soto
Tim Spector
David St Clair
Christine Stevens
Nathan O. Stitziel
From the Cardiovascular Division, Department of Medicine, and the Department of Genetics, Washington University School of Medicine, St. Louis.
Patrick F. Sullivan
Jaana Suvisaari
E. Shyong Tai
Michael E. Talkowski
Yekaterina Tarasova
Kent D. Taylor
The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA.
Yik Ying Teo
Grace Tiao
Kathleen Tibbetts
Charlotte Tolonen
Ming Tsuang
Tiinamaija Tuomi
Dan Turner
Teresa Tusie-Luna
Erkki Vartiainen
Marquis Vawter
Séverine Vermeire
Elisabet Vilella
Christopher Vittal
Gordon Wade
Mark Walker
Arcturus Wang
Lily Wang
Qingbo Wang
James S. Ware
Hugh Watkins
Nicholas A. Watts
Rinse K. Weersma
Ben Weisburd
Maija Wessman
Christopher Whelan
Nicola Whiffin
James G. Wilson
Lauren Witzgall
Ramnik J. Xavier
Mary T. Yohannes
Robert Yolken
Xuefang Zhao
Tuuli Lappalainen
Heidi L. Rehm
Daniel G. MacArthur
Anne O’Donnell-Luria