Exploring penetrance of clinically relevant variants in over 800,000 humans from the Genome Aggregation Database

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

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

Volume / Issue Vol. 16, Issue 1
Published October 31, 2025
ISSN 2041-1723
Publisher Nature Portfolio

Journal Info

Nature Communications

Nature Portfolio

ISSN: 2041-1723 Open Access Life Sciences

Authors (306)

M

Moriel Singer-Berk

S

Sarah L. Stenton

J

Julia K. Goodrich

M

Michael W. Wilson

J

Jonah Einson

M

Maria Abreu

A

Amina Abubakar

R

Rolf Adolfsson

C

Carlos A. Aguilar Salinas

T

Tariq Ahmad

C

Christine M. Albert

Department of Cardiology, Smidt Heart Institute, Cedars–Sinai Medical Center, Los Angeles

J

Jessica Alföldi

M

Matthieu Allez

C

Celso Arango López

D

Diego Ardissino

I

Irina M. Armean

E

Elizabeth G. Atkinson

G

Gil Atzmon

E

Eric Banks

J

John Barnard

S

Samantha M. Baxter

L

Laurent Beaugerie

D

David Benjamin

E

Emelia J. Benjamin

L

Louis Bergelson

C

Charles Bernstein

D

Douglas Blackwood

M

Michael Boehnke

L

Lori L. Bonnycastle

E

Erwin P. Bottinger

D

Donald W. Bowden

M

Matthew J. Bown

H

Harrison Brand

S

Steven Brant

T

Ted Brookings

S

Sam Bryant

S

Shawneequa L. Callier

H

Hannia Campos

J

John C. Chambers

J

Juliana C. Chan

K

Katherine R. Chao

S

Sinéad Chapman

D

Daniel I. Chasman

L

Lea A. Chen

S

Siwei Chen

R

Rex Chisholm

J

Judy Cho

R

Rajiv Chowdhury

M

Mina K. Chung

W

Wendy K. Chung

Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School

K

Kristian Cibulskis

B

Bruce Cohen

R

Ryan L. Collins

K

Kristen M. Connolly

A

Adolfo Correa

A

Aiden Corvin

M

Miguel Covarrubias

N

Nick Craddock

B

Beryl B. Cummings

D

Dana Dabelea

M

Mark J. Daly

J

John Danesh

D

Dawood Darbar

P

Phil Darnowsky

J

Joshua C. Denny

S

Stacey Donnelly

R

Richard H. Duerr

R

Ravindranath Duggirala

J

Josée Dupuis

P

Patrick T. Ellinor

R

Roberto Elosua

J

James Emery

E

Eleina England

J

Jeanette Erdmann

T

Tõnu Esko

E

Emily Evangelista

Y

Yossi Farjoun

D

Diane Fatkin

W

William Faubion

S

Steven Ferriera

G

Gemma Figtree

K

Kelly Flannagan

J

Jose Florez

L

Laurent Francioli

A

Andre Franke

A

Adam Frankish

J

Jack Fu

M

Martti Färkkilä

S

Stacey Gabriel

K

Kiran Garimella

L

Laura D. Gauthier

J

Jeff Gentry

M

Michel Georges

G

Gad Getz

D

David C. Glahn

B

Benjamin Glaser

S

Stephen J. Glatt

F

Fernando S. Goes

D

David Goldstein

C

Clicerio Gonzalez

J

Julia Goodrich

R

Riley H. Grant

L

Leif Groop

S

Sanna Gudmundsson

N

Namrata Gupta

Broad Institute of MIT and Harvard, Cambridge, MA, USA.

A

Andrea Haessly

C

Christopher Haiman

I

Ira Hall

C

Craig L. Hanis

J

James Hanyok

M

Matthew Harms

Q

Qin He

State Key Laboratory of Soil Pollution Control and Safety, Department of Chemistry

M

Mikko Hiltunen

M

Matti M. Holi

C

Christina M. Hultman

S

Steve Jahl

C

Chaim Jalas

T

Thibault Jeandet

M

Mikko Kallela

D

Diane Kaplan

J

Jaakko Kaprio

K

Konrad J. Karczewski

E

Elizabeth W. Karlson

S

Sekar Kathiresan

Verve Therapeutics, a wholly owned subsidiary of Eli Lilly, Boston

E

Eimear E. Kenny

B

Bong-Jo Kim

Y

Young Jin Kim

D

Daniel King

G

George Kirov

Z

Zan Koenig

J

Jaspal Kooner

S

Seppo Koskinen

H

Harlan M. Krumholz

S

Subra Kugathasan

J

Juozas Kupcinskas

S

Soo Heon Kwak

M

Markku Laakso

N

Nicole Lake

M

Mikael Landén

T

Trevyn Langsford

K

Kristen M. Laricchia

T

Terho Lehtimäki

M

Monkol Lek

Department of Genetics, Yale School of Medicine

J

James Lewis

C

Cecilia M. Lindgren

E

Emily Lipscomb

C

Christopher Llanwarne

R

Ruth J. F. Loos

E

Edouard Louis

C

Chelsea Lowther

W

Wenhan Lu

S

Steven A. Lubitz

T

Tom Lyons

R

Ronald C. W. Ma

D

Dara S. Manoach

G

Gregory M. Marcus

Division of Cardiology, University of California, San Francisco, San Francisco

J

Jaume Marrugat

N

Nicholas Marston

D

Daniel M. Marten

A

Alicia R. Martin

K

Kari M. Mattila

S

Steven McCarroll

M

Mark I. McCarthy

J

Jacob L. McCauley

D

Dermot McGovern

R

Ruth McPherson

A

Andrew MacQuillin

J

James B. Meigs

O

Olle Melander

A

Andres Metspalu

D

Deborah Meyers

E

Eric V. Minikel

B

Braxton D. Mitchell

P

Paul Moayyedi

Farncombe Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada

S

Sanghamitra Mohanty

A

Andrés Moreno Estrada

N

Nicola J. Mulder

R

Ruchi Munshi

A

Aliya Naheed

A

Andrea Natale

Texas Cardiac Arrhythmia Research, St. David’s Medical Center, Austin

S

Saman Nazarian

B

Benjamin M. Neale

C

Charles Newton

P

Peter M. Nilsson

S

Sam Novod

A

Anne H. O’Donnell-Luria

M

Michael C. O’Donovan

Y

Yukinori Okada

D

Dost Ongur

R

Roel Ophoff

L

Lorena Orozco

W

Willem Ouwehand

M

Michael J. Owen

N

Nick Owen

C

Colin Palmer

N

Nicholette D. Palmer

A

Aarno Palotie

M

Mara Parellada

K

Kyong Soo Park

C

Carlos Pato

N

Nancy L. Pedersen

T

Tina Pesaran

N

Nikelle Petrillo

W

William Phu

S

Sharon Plon

D

Danielle Posthuma

T

Timothy Poterba

A

Ann E. Pulver

A

Aaron Quinlan

D

Dan Rader

N

Nazneen Rahman

H

Heidi Rehm

A

Andreas Reif

A

Alex Reiner

Department of Epidemiology, University of Washington, Seattle, WA, USA.

A

Anne M. Remes

D

Dan Rhodes

S

Stephen Rich

J

John D. Rioux

S

Samuli Ripatti

D

David Roazen

J

Jason Roberts

E

Elise Robinson

Molecular Imaging Program at Stanford, Department of Radiology, School of Medicine, Stanford University

D

Dan M. Roden

J

Jerome I. Rotter

G

Guy Rouleau

V

Valentin Ruano-Rubio

C

Christian T. Ruff

H

Heiko Runz

M

Marc S. Sabatine

TIMI Study Group, Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston

N

Nareh Sahakian

D

Danish Saleheen

V

Veikko Salomaa

A

Andrea Saltzman

N

Nilesh J. Samani

K

Kaitlin E. Samocha

A

Alba Sanchis-Juan

A

Akira Sawa

J

Jeremiah Scharf

M

Molly Schleicher

P

Patrick Schultz

H

Heribert Schunkert

DZHK Partner Site Munich, Munich Heart Alliance, Munich, Germany

S

Sebastian Schönherr

E

Eleanor G. Seaby

C

Cotton Seed

S

Svati H. Shah

M

Megan Shand

T

Ted Sharpe

M

Moore B. Shoemaker

T

Tai Shyong

E

Edwin K. Silverman

Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA.

J

Jurgita Skiecevičienė

P

Pamela Sklar

J

J. Gustav Smith

J

Jonathan T. Smith

J

Jordan Smoller

H

Hilkka Soininen

H

Harry Sokol

M

Matthew Solomonson

R

Rachel G. Son

J

Jose Soto

T

Tim Spector

D

David St Clair

C

Christine Stevens

N

Nathan O. Stitziel

From the Cardiovascular Division, Department of Medicine, and the Department of Genetics, Washington University School of Medicine, St. Louis.

P

Patrick F. Sullivan

J

Jaana Suvisaari

E

E. Shyong Tai

M

Michael E. Talkowski

Y

Yekaterina Tarasova

K

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.

Y

Yik Ying Teo

G

Grace Tiao

K

Kathleen Tibbetts

C

Charlotte Tolonen

M

Ming Tsuang

T

Tiinamaija Tuomi

D

Dan Turner

T

Teresa Tusie-Luna

E

Erkki Vartiainen

M

Marquis Vawter

S

Séverine Vermeire

E

Elisabet Vilella

C

Christopher Vittal

G

Gordon Wade

M

Mark Walker

A

Arcturus Wang

L

Lily Wang

Q

Qingbo Wang

J

James S. Ware

H

Hugh Watkins

N

Nicholas A. Watts

R

Rinse K. Weersma

B

Ben Weisburd

M

Maija Wessman

C

Christopher Whelan

N

Nicola Whiffin

J

James G. Wilson

L

Lauren Witzgall

R

Ramnik J. Xavier

M

Mary T. Yohannes

R

Robert Yolken

X

Xuefang Zhao

T

Tuuli Lappalainen

H

Heidi L. Rehm

D

Daniel G. MacArthur

A

Anne O’Donnell-Luria