Bi-allelic ATG4D variants are associated with a neurodevelopmental disorder characterized by speech and motor impairment
Authors: Morimoto Marie , Bhambhani Vikas , Gazzaz Nour , Davids Mariska , Sathiyaseelan Paalini , Macnamara Ellen F. , Lange Jennifer , Lehman Anna , Zerfas Patricia M. , Murphy Jennifer L. , Acosta Maria T. , Wang Camille , Alderman Emily ,   Undiagnosed Diseases Network, Adam Margaret , Alvarez Raquel L. , Alvey Justin , Amendola Laura , Andrews Ashley , Ashley Euan A. , Azamian Mahshid S. , Bacino Carlos A. , Bademci Guney , Balasubramanyam Ashok , Baldridge Dustin , Bale Jim , Bamshad Michael , Barbouth Deborah , Bayrak-Toydemir Pinar , Beck Anita , Beggs Alan H. , Behrens Edward , Bejerano Gill , Bellen Hugo J. , Bennett Jimmy , Berg-Rood Beverly , Bernstein Jonathan A. , Berry Gerard T. , Bican Anna , Bivona Stephanie , Blue Elizabeth , Bohnsack John , Bonner Devon , Botto Lorenzo , Boyd Brenna , Briere Lauren C. , Brokamp Elly , Brown Gabrielle , Burke Elizabeth A. , Burrage Lindsay C. , Butte Manish J. , Byers Peter , Byrd William E. , Carey John , Carrasquillo Olveen , Cassini Thomas , Chang Ta Chen Peter , Chanprasert Sirisak , Chao Hsiao-Tuan , Clark Gary D. , Coakley Terra R. , Cobban Laurel A. , Cogan Joy D. , Coggins Matthew , Cole F. Sessions , Colley Heather A. , Cooper Cynthia M. , Cope Heidi , Craigen William J. , Crouse Andrew B. , Cunningham Michael , D’Souza Precilla , Dai Hongzheng , Dasari Surendra , Davis Joie , Dayal Jyoti G. , Dell’Angelica Esteban C. , Dipple Katrina , Doherty Daniel , Dorrani Naghmeh , Doss Argenia L. , Douine Emilie D. , Duncan Laura , Earl Dawn , Eckstein David J. , Emrick Lisa T. , Eng Christine M. , Esteves Cecilia , Falk Marni , Fieg Elizabeth L. , Fisher Paul G. , Fogel Brent L. , Forghani Irman , Glass Ian , Gochuico Bernadette , Goddard Page C. , Godfrey Rena A. , Golden-Grant Katie , Grajewski Alana , Gutierrez Irma , Hadley Don , Hahn Sihoun , Halley Meghan C. , Hamid Rizwan , Hassey Kelly , Hayes Nichole , High Frances , Hing Anne , Hisama Fuki M. , Holm Ingrid A. , Hom Jason , Horike-Pyne Martha , Huang Alden , Hutchison Sarah , Introne Wendy J. , Isasi Rosario , Izumi Kosuke , Jamal Fariha , Jarvik Gail P. , Jarvik Jeffrey , Jayadev Suman , Jean-Marie Orpa , Jobanputra Vaidehi , Karaviti Lefkothea , Kennedy Jennifer , Ketkar Shamika , Kiley Dana , Kilich Gonench , Kobren Shilpa N. , Kohane Isaac S. , Kohler Jennefer N. , Korrick Susan , Kozuira Mary , Krakow Deborah , Krasnewich Donna M. , Kravets Elijah , Lalani Seema R. , Lam Byron , Lam Christina , Lanpher Brendan C. , Lanza Ian R. , LeBlanc Kimberly , Lee Brendan H. , Levitt Roy , Lewis Richard A. , Liu Pengfei , Liu Xue Zhong , Longo Nicola , Loo Sandra K. , Loscalzo Joseph , Maas Richard L. , MacRae Calum A. , Maduro Valerie V. , Mahoney Rachel , Mak Bryan C. , Mamounas Laura A. , Manolio Teri A. , Mao Rong , Maravilla Kenneth , Marom Ronit , Marth Gabor , Martin Beth A. , Martin Martin G. , Martínez-Agosto Julian A. , Marwaha Shruti , McCauley Jacob , McConkie-Rosell Allyn , McCray Alexa T. , McGee Elisabeth , Mefford Heather , Merritt J. Lawrence , Might Matthew , Mirzaa Ghayda , Morava Eva , Moretti Paolo , Nakano-Okuno Mariko , Nelson Stanley F. , Newman John H. , Nicholas Sarah K. , Nickerson Deborah , Nieves-Rodriguez Shirley , Novacic Donna , Oglesbee Devin , Orengo James P. , Pace Laura , Pak Stephen , Pallais J. Carl , Palmer Christina G. S. , Papp Jeanette C. , Parker Neil H. , Phillips John A. , Posey Jennifer E. , Potocki Lorraine , Pusey Swerdzewski Barbara N. , Quinlan Aaron , Rao Deepak A. , Raper Anna , Raskind Wendy , Renteria Genecee , Reuter Chloe M. , Rives Lynette , Robertson Amy K. , Rodan Lance H. , Rosenfeld Jill A. , Rosenwasser Natalie , Rossignol Francis , Ruzhnikov Maura , Sacco Ralph , Sampson Jacinda B. , Saporta Mario , Schaechter Judy , Schedl Timothy , Schoch Kelly , Scott Daryl A. , Scott C. Ron , Shashi Vandana , Shin Jimann , Silverman Edwin K. , Sinsheimer Janet S. , Sisco Kathy , Smith Edward C. , Smith Kevin S. , Solem Emily , Solnica-Krezel Lilianna , Solomon Benjamin , Spillmann Rebecca C. , Stoler Joan M. , Sullivan Kathleen , Sullivan Jennifer A. , Sun Angela , Sutton Shirley , Sweetser David A. , Sybert Virginia , Tabor Holly K. , Tan Queenie K.-G. , Tan Amelia L. M. , Tekin Mustafa , Telischi Fred , Thorson Willa , Toro Camilo , Tran Alyssa A. , Ungar Rachel A. , Urv Tiina K. , Vanderver Adeline , Velinder Matt , Viskochil Dave , Vogel Tiphanie P. , Wahl Colleen E. , Walker Melissa , Wallace Stephanie , Walley Nicole M. , Wambach Jennifer , Wan Jijun , Wang Lee-Kai , Wangler Michael F. , Ward Patricia A. , Wegner Daniel , Weisz Hubshman Monika , Wener Mark , Wenger Tara , Wesseling Perry Katherine , Westerfield Monte , Wheeler Matthew T. , Whitlock Jordan , Wolfe Lynne A. , Worley Kim , Xiao Changrui , Yamamoto Shinya , Yang John , Zhang Zhe , Zuchner Stephan , Reichert Sara , Thurm Audrey , Adams David R. , Introne Wendy J. , Gorski Sharon M. , Boerkoel Cornelius F. , Gahl William A. , Tifft Cynthia J. , Malicdan May Christine V. 
Published: February 2023

Autophagy regulates the degradation of damaged organelles and protein aggregates, and is critical for neuronal development, homeostasis, and maintenance, yet few neurodevelopmental disorders have been associated with pathogenic variants in genes encoding autophagy-related proteins. We report three individuals from two unrelated families with a neurodevelopmental disorder characterized by speech and motor impairment, and similar facial characteristics. Rare, conserved, bi-allelic variants were identified in ATG4D, encoding one of four ATG4 cysteine proteases important for autophagosome biogenesis, a hallmark of autophagy. Autophagosome biogenesis and induction of autophagy were intact in cells from affected individuals. However, studies evaluating the predominant substrate of ATG4D, GABARAPL1, demonstrated that three of the four ATG4D patient variants functionally impair ATG4D activity. GABARAPL1 is cleaved or “primed” by ATG4D and an in vitro GABARAPL1 priming assay revealed decreased priming activity for three of the four ATG4D variants. Furthermore, a rescue experiment performed in an ATG4 tetra knockout cell line, in which all four ATG4 isoforms were knocked out by gene editing, showed decreased GABARAPL1 priming activity for the two ATG4D missense variants located in the cysteine protease domain required for priming, suggesting that these variants impair the function of ATG4D. The clinical, bioinformatic, and functional data suggest that bi-allelic loss-of-function variants in ATG4D contribute to the pathogenesis of this syndromic neurodevelopmental disorder.