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Chen Y, Dawes R, Kim HC, Stenton SL, Walker S, Ljungdahl A, Lord J, Ganesh VS, Ma J, Martin-Geary AC, Lemire G, D'Souza EN, Dong S, Ellingford JM, Adams DR, Allan K, Bakshi M, Baldwin EE, Berger SI, Bernstein JA, Brown NJ, Burrage LC, Chapman K, Compton AG, Cunningham CA, D'Souza P, Délot EC, Dias KR, Elias ER, Evans CA, Ewans L, Ezell K, Fraser JL, Gallacher L, Genetti CA, Grant CL, Haack T, Kuechler A, Lalani SR, Leitão E, Fevre AL, Leventer RJ, Liebelt JE, Lockhart PJ, Ma AS, Macnamara EF, Maurer TM, Mendez HR, Montgomery SB, Nassogne MC, Neumann S, O'Leary M, Palmer EE, Phillips J, Pitsava G, Pysar R, Rehm HL, Reuter CM, Revencu N, Riess A, Rius R, Rodan L, Roscioli T, Rosenfeld JA, Sachdev R, Simons C, Sisodiya SM, Snell P, Clair LS, Stark Z, Tan TY, Tan NB, Temple SE, Thorburn DR, Tifft CJ, Uebergang E, VanNoy GE, Vilain E, Viskochil DH, Wedd L, Wheeler MT, White SM, Wojcik M, Wolfe LA, Wolfenson Z, Xiao C, Zocche D, Rubenstein JL, Markenscoff-Papadimitriou E, Fica SM, Baralle D, Depienne C, MacArthur DG, Howson JM, Sanders SJ, O'Donnell-Luria A, Whiffin N. De novo variants in the non-coding spliceosomal snRNA gene RNU4-2 are a frequent cause of syndromic neurodevelopmental disorders. medRxiv 2024:2024.04.07.24305438. [PMID: 38645094 PMCID: PMC11030480 DOI: 10.1101/2024.04.07.24305438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Around 60% of individuals with neurodevelopmental disorders (NDD) remain undiagnosed after comprehensive genetic testing, primarily of protein-coding genes 1 . Increasingly, large genome-sequenced cohorts are improving our ability to discover new diagnoses in the non-coding genome. Here, we identify the non-coding RNA RNU4-2 as a novel syndromic NDD gene. RNU4-2 encodes the U4 small nuclear RNA (snRNA), which is a critical component of the U4/U6.U5 tri-snRNP complex of the major spliceosome 2 . We identify an 18 bp region of RNU4-2 mapping to two structural elements in the U4/U6 snRNA duplex (the T-loop and Stem III) that is severely depleted of variation in the general population, but in which we identify heterozygous variants in 119 individuals with NDD. The vast majority of individuals (77.3%) have the same highly recurrent single base-pair insertion (n.64_65insT). We estimate that variants in this region explain 0.41% of individuals with NDD. We demonstrate that RNU4-2 is highly expressed in the developing human brain, in contrast to its contiguous counterpart RNU4-1 and other U4 homologs, supporting RNU4-2 's role as the primary U4 transcript in the brain. Overall, this work underscores the importance of non-coding genes in rare disorders. It will provide a diagnosis to thousands of individuals with NDD worldwide and pave the way for the development of effective treatments for these individuals.
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2
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Macnamara EF, Loydpierson A, Latour YL, D'Souza P, Murphy J, Wolfe L, Estwick T, Johnston JM, Yang J, Acosta MT, Lee PR, Pierson TM, Soldatos A, Toro C, Markello T, Adams DR, Gahl WA, Yousef M, Tifft CJ. Risks and benefits of anesthesia for combined pediatric procedures in the NIH undiagnosed diseases program. Mol Genet Metab 2023; 140:107707. [PMID: 37883914 DOI: 10.1016/j.ymgme.2023.107707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/06/2023] [Accepted: 10/07/2023] [Indexed: 10/28/2023]
Abstract
PURPOSE The NIH Undiagnosed Diseases Program (UDP) aims to provide diagnoses to patients who have previously received exhaustive evaluations yet remain undiagnosed. Patients undergo procedural anesthesia for deep phenotyping for analysis with genomic testing. METHODS A retrospective chart review was performed to determine the safety and benefit of procedural anesthesia in pediatric patients in the UDP. Adverse perioperative events were classified as anesthesia-related complications or peri-procedural complications. The contribution of procedures performed under anesthesia to arriving at a diagnosis was also determined. RESULTS From 2008 to 2020, 249 pediatric patients in the UDP underwent anesthesia for diagnostic procedures. The majority had a severe systemic disease (American Society for Anesthesiology status III, 79%) and/or a neurologic condition (91%). Perioperative events occurred in 45 patients; six of these were attributed to anesthesia. All patients recovered fully without sequelae. Nearly half of the 249 patients (49%) received a diagnosis, and almost all these diagnoses (88%) took advantage of information gleaned from procedures performed under anesthesia. CONCLUSIONS The benefits of anesthesia involving multiple diagnostic procedures in a well-coordinated, multidisciplinary, research setting, such as in the pediatric UDP, outweigh the risks.
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Affiliation(s)
- Ellen F Macnamara
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America
| | - Amelia Loydpierson
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America; University of North Carolina School of Medicine, Chapel Hill, NC, United States of America
| | - Yvonne L Latour
- Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, United States of America; Department of Pathology, Immunology, and Microbiology, Vanderbilt University, Nashville, TN, United States of America
| | - Precilla D'Souza
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America; Hummingbird House Children's Hospice, 60 Curwen Terrace, Chermside, Queensland 4032, Australia
| | - Jennifer Murphy
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America; Hummingbird House Children's Hospice, 60 Curwen Terrace, Chermside, Queensland 4032, Australia
| | - Lynne Wolfe
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America
| | - Tyra Estwick
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America; Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, United States of America
| | - Jean M Johnston
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America
| | - John Yang
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America
| | - Maria T Acosta
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America
| | - Paul R Lee
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America; Division of Neurology 2, Office of Neuroscience, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States of America
| | - Tyler Mark Pierson
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America; Departments of Pediatrics and Neurology & The Board of Governors, Regenerative Medicine Institute and the Cedars Sinai Center for the Undiagnosed Patient, Cedars Sinai Medical Center, Los Angeles, CA, United States of America
| | - Ariane Soldatos
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, United States of America
| | - Camilo Toro
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America
| | - Tom Markello
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America
| | - David R Adams
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America; National Human Genome Research Institute, NIH, Bethesda, MD, United States of America
| | - William A Gahl
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America
| | - Muhammad Yousef
- National Institutes of Health Clinical Center, Department of Perioperative Medicine, Pediatric Anesthesiology, Bethesda, MD, United States of America
| | - Cynthia J Tifft
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD, United States of America; National Human Genome Research Institute, NIH, Bethesda, MD, United States of America.
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3
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Tinker RJ, Bastarache L, Ezell K, Kobren SN, Esteves C, Rosenfeld JA, Macnamara EF, Hamid R, Cogan JD, Rinker D, Mukharjee S, Glass I, Dipple K, Phillips JA. The contribution of mosaicism to genetic diseases and de novo pathogenic variants. Am J Med Genet A 2023; 191:2482-2492. [PMID: 37246601 DOI: 10.1002/ajmg.a.63309] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/29/2023] [Accepted: 05/03/2023] [Indexed: 05/30/2023]
Abstract
The contribution of mosaicism to diagnosed genetic disease and presumed de novo variants (DNV) is under investigated. We determined the contribution of mosaic genetic disease (MGD) and diagnosed parental mosaicism (PM) in parents of offspring with reported DNV (in the same variant) in the (1) Undiagnosed Diseases Network (UDN) (N = 1946) and (2) in 12,472 individuals electronic health records (EHR) who underwent genetic testing at an academic medical center. In the UDN, we found 4.51% of diagnosed probands had MGD, and 2.86% of parents of those with DNV exhibited PM. In the EHR, we found 6.03% and 2.99% and (of diagnosed probands) had MGD detected on chromosomal microarray and exome/genome sequencing, respectively. We found 2.34% (of those with a presumed pathogenic DNV) had a parent with PM for the variant. We detected mosaicism (regardless of pathogenicity) in 4.49% of genetic tests performed. We found a broad phenotypic spectrum of MGD with previously unknown phenotypic phenomena. MGD is highly heterogeneous and provides a significant contribution to genetic diseases. Further work is required to improve the diagnosis of MGD and investigate how PM contributes to DNV risk.
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Affiliation(s)
- Rory J Tinker
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kimberly Ezell
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Cecilia Esteves
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ellen F Macnamara
- Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Rizwan Hamid
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Joy D Cogan
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - David Rinker
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Souhrid Mukharjee
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Ian Glass
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Katrina Dipple
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - John A Phillips
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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4
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Srivastava S, Shaked HM, Gable K, Gupta SD, Pan X, Somashekarappa N, Han G, Mohassel P, Gotkine M, Doney E, Goldenberg P, Tan QKG, Gong Y, Kleinstiver B, Wishart B, Cope H, Pires CB, Stutzman H, Spillmann RC, Sadjadi R, Elpeleg O, Lee CH, Bellen HJ, Edvardson S, Eichler F, Dunn TM, Dai H, Dhar SU, Emrick LT, Goldman AM, Hanchard NA, Jamal F, Karaviti L, Lalani SR, Lee BH, Lewis RA, Marom R, Moretti PM, Murdock DR, Nicholas SK, Orengo JP, Posey JE, Potocki L, Rosenfeld JA, Samson SL, Scott DA, Tran AA, Vogel TP, Wangler MF, Yamamoto S, Eng CM, Liu P, Ward PA, Behrens E, Deardorff M, Falk M, Hassey K, Sullivan K, Vanderver A, Goldstein DB, Cope H, McConkie-Rosell A, Schoch K, Shashi V, Smith EC, Spillmann RC, Sullivan JA, Tan QKG, Walley NM, Agrawal PB, Beggs AH, Berry GT, Briere LC, Cobban LA, Coggins M, Cooper CM, Fieg EL, High F, Holm IA, Korrick S, Krier JB, Lincoln SA, Loscalzo J, Maas RL, MacRae CA, Pallais JC, Rao DA, Rodan LH, Silverman EK, Stoler JM, Sweetser DA, Walker M, Walsh CA, Esteves C, Kelley EG, Kohane IS, LeBlanc K, McCray AT, Nagy A, Dasari S, Lanpher BC, Lanza IR, Morava E, Oglesbee D, Bademci G, Barbouth D, Bivona S, Carrasquillo O, Chang TCP, Forghani I, Grajewski A, Isasi R, Lam B, Levitt R, Liu XZ, McCauley J, Sacco R, Saporta M, Schaechter J, Tekin M, Telischi F, Thorson W, Zuchner S, Colley HA, Dayal JG, Eckstein DJ, Findley LC, Krasnewich DM, Mamounas LA, Manolio TA, Mulvihill JJ, LaMoure GL, Goldrich MP, Urv TK, Doss AL, Acosta MT, Bonnenmann C, D’Souza P, Draper DD, Ferreira C, Godfrey RA, Groden CA, Macnamara EF, Maduro VV, Markello TC, Nath A, Novacic D, Pusey BN, Toro C, Wahl CE, Baker E, Burke EA, Adams DR, Gahl WA, Malicdan MCV, Tifft CJ, Wolfe LA, Yang J, Power B, Gochuico B, Huryn L, Latham L, Davis J, Mosbrook-Davis D, Rossignol F, Solomon B, MacDowall J, Thurm A, Zein W, Yousef M, Adam M, Amendola L, Bamshad M, Beck A, Bennett J, Berg-Rood B, Blue E, Boyd B, Byers P, Chanprasert S, Cunningham M, Dipple K, Doherty D, Earl D, Glass I, Golden-Grant K, Hahn S, Hing A, Hisama FM, Horike-Pyne M, Jarvik GP, Jarvik J, Jayadev S, Lam C, Maravilla K, Mefford H, Merritt JL, Mirzaa G, Nickerson D, Raskind W, Rosenwasser N, Scott CR, Sun A, Sybert V, Wallace S, Wener M, Wenger T, Ashley EA, Bejerano G, Bernstein JA, Bonner D, Coakley TR, Fernandez L, Fisher PG, Fresard L, Hom J, Huang Y, Kohler JN, Kravets E, Majcherska MM, Martin BA, Marwaha S, McCormack CE, Raja AN, Reuter CM, Ruzhnikov M, Sampson JB, Smith KS, Sutton S, Tabor HK, Tucker BM, Wheeler MT, Zastrow DB, Zhao C, Byrd WE, Crouse AB, Might M, Nakano-Okuno M, Whitlock J, Brown G, Butte MJ, Dell’Angelica EC, Dorrani N, Douine ED, Fogel BL, Gutierrez I, Huang A, Krakow D, Lee H, Loo SK, Mak BC, Martin MG, Martínez-Agosto JA, McGee E, Nelson SF, Nieves-Rodriguez S, Palmer CGS, Papp JC, Parker NH, Renteria G, Signer RH, Sinsheimer JS, Wan J, Wang LK, Perry KW, Woods JD, Alvey J, Andrews A, Bale J, Bohnsack J, Botto L, Carey J, Pace L, Longo N, Marth G, Moretti P, Quinlan A, Velinder M, Viskochi D, Bayrak-Toydemir P, Mao R, Westerfield M, Bican A, Brokamp E, Duncan L, Hamid R, Kennedy J, Kozuira M, Newman JH, PhillipsIII JA, Rives L, Robertson AK, Solem E, Cogan JD, Cole FS, Hayes N, Kiley D, Sisco K, Wambach J, Wegner D, Baldridge D, Pak S, Schedl T, Shin J, Solnica-Krezel L, Sadjadi R, Elpeleg O, Lee CH, Bellen HJ, Edvardson S, Eichler F, Dunn TM. SPTSSA variants alter sphingolipid synthesis and cause a complex hereditary spastic paraplegia. Brain 2023; 146:1420-1435. [PMID: 36718090 PMCID: PMC10319774 DOI: 10.1093/brain/awac460] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/03/2022] [Accepted: 11/19/2022] [Indexed: 02/01/2023] Open
Abstract
Sphingolipids are a diverse family of lipids with critical structural and signalling functions in the mammalian nervous system, where they are abundant in myelin membranes. Serine palmitoyltransferase, the enzyme that catalyses the rate-limiting reaction of sphingolipid synthesis, is composed of multiple subunits including an activating subunit, SPTSSA. Sphingolipids are both essential and cytotoxic and their synthesis must therefore be tightly regulated. Key to the homeostatic regulation are the ORMDL proteins that are bound to serine palmitoyltransferase and mediate feedback inhibition of enzymatic activity when sphingolipid levels become excessive. Exome sequencing identified potential disease-causing variants in SPTSSA in three children presenting with a complex form of hereditary spastic paraplegia. The effect of these variants on the catalytic activity and homeostatic regulation of serine palmitoyltransferase was investigated in human embryonic kidney cells, patient fibroblasts and Drosophila. Our results showed that two different pathogenic variants in SPTSSA caused a hereditary spastic paraplegia resulting in progressive motor disturbance with variable sensorineural hearing loss and language/cognitive dysfunction in three individuals. The variants in SPTSSA impaired the negative regulation of serine palmitoyltransferase by ORMDLs leading to excessive sphingolipid synthesis based on biochemical studies and in vivo studies in Drosophila. These findings support the pathogenicity of the SPTSSA variants and point to excessive sphingolipid synthesis due to impaired homeostatic regulation of serine palmitoyltransferase as responsible for defects in early brain development and function.
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Affiliation(s)
- Siddharth Srivastava
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, BostonChildren's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hagar Mor Shaked
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Kenneth Gable
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Sita D Gupta
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Niranjanakumari Somashekarappa
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Gongshe Han
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
| | - Marc Gotkine
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | | | - Paula Goldenberg
- Department of Pediatrics, Section on Medical Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Queenie K G Tan
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yi Gong
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Benjamin Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Brian Wishart
- Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Heidi Cope
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Claudia Brito Pires
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Hannah Stutzman
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rebecca C Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Reza Sadjadi
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Simon Edvardson
- Pediatric Neurology Unit, Hadassah University Hospital, Mount Scopus, Jerusalem 91240, Israel
| | - Florian Eichler
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Teresa M Dunn
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
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- Department of Neurology, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02114 , USA
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem , Jerusalem 91120 , Israel
| | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children’s Research Hospital , Memphis, TN 38105 , USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX 77030 , USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital , Houston, TX 77030 , USA
| | - Simon Edvardson
- Pediatric Neurology Unit, Hadassah University Hospital, Mount Scopus , Jerusalem 91240 , Israel
| | - Florian Eichler
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02114 , USA
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02114 , USA
| | - Teresa M Dunn
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences , Bethesda, MD 20814 , USA
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5
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Frost FG, Morimoto M, Sharma P, Ruaud L, Belnap N, Calame DG, Uchiyama Y, Matsumoto N, Oud MM, Ferreira EA, Narayanan V, Rangasamy S, Huentelman M, Emrick LT, Sato-Shirai I, Kumada S, Wolf NI, Steinbach PJ, Huang Y, Pusey BN, Passemard S, Levy J, Drunat S, Vincent M, Guet A, Agolini E, Novelli A, Digilio MC, Rosenfeld JA, Murphy JL, Lupski JR, Vezina G, Macnamara EF, Adams DR, Acosta MT, Tifft CJ, Gahl WA, Malicdan MCV. Bi-allelic SNAPC4 variants dysregulate global alternative splicing and lead to neuroregression and progressive spastic paraparesis. Am J Hum Genet 2023; 110:663-680. [PMID: 36965478 PMCID: PMC10119142 DOI: 10.1016/j.ajhg.2023.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/28/2023] [Indexed: 03/27/2023] Open
Abstract
The vast majority of human genes encode multiple isoforms through alternative splicing, and the temporal and spatial regulation of those isoforms is critical for organismal development and function. The spliceosome, which regulates and executes splicing reactions, is primarily composed of small nuclear ribonucleoproteins (snRNPs) that consist of small nuclear RNAs (snRNAs) and protein subunits. snRNA gene transcription is initiated by the snRNA-activating protein complex (SNAPc). Here, we report ten individuals, from eight families, with bi-allelic, deleterious SNAPC4 variants. SNAPC4 encoded one of the five SNAPc subunits that is critical for DNA binding. Most affected individuals presented with delayed motor development and developmental regression after the first year of life, followed by progressive spasticity that led to gait alterations, paraparesis, and oromotor dysfunction. Most individuals had cerebral, cerebellar, or basal ganglia volume loss by brain MRI. In the available cells from affected individuals, SNAPC4 abundance was decreased compared to unaffected controls, suggesting that the bi-allelic variants affect SNAPC4 accumulation. The depletion of SNAPC4 levels in HeLa cell lines via genomic editing led to decreased snRNA expression and global dysregulation of alternative splicing. Analysis of available fibroblasts from affected individuals showed decreased snRNA expression and global dysregulation of alternative splicing compared to unaffected cells. Altogether, these data suggest that these bi-allelic SNAPC4 variants result in loss of function and underlie the neuroregression and progressive spasticity in these affected individuals.
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Affiliation(s)
- F Graeme Frost
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Marie Morimoto
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Prashant Sharma
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Lyse Ruaud
- APHP.Nord, Robert Debré University Hospital, Department of Genetics, Paris, France; Université Paris Cité, Inserm UMR 1141, NeuroDiderot, 75019 Paris, France
| | - Newell Belnap
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Daniel G Calame
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Yuri Uchiyama
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan; Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Machteld M Oud
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Elise A Ferreira
- Department of Pediatrics, Emma Children's Hospital, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, Amsterdam, the Netherlands; United for Metabolic Diseases, Amsterdam, the Netherlands
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Sampath Rangasamy
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Matt Huentelman
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Lisa T Emrick
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Ikuko Sato-Shirai
- Department of Neuropediatrics, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan; Department of Pediatrics, Shimada Ryoiku Medical Center Hachioji for Challenged Children, Tokyo, Japan
| | - Satoko Kumada
- Department of Neuropediatrics, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - Nicole I Wolf
- Amsterdam Leukodystrophy Center, Department of Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centers, and Amsterdam Neuroscience, Cellular & Molecular Mechanisms, Vrije Universiteit, Amsterdam, the Netherlands
| | - Peter J Steinbach
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yan Huang
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Barbara N Pusey
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Sandrine Passemard
- Université Paris Cité, Inserm UMR 1141, NeuroDiderot, 75019 Paris, France; Service de Neurologie Pédiatrique, DMU INOV-RDB, APHP, Hôpital Robert Debré, Paris, France
| | - Jonathan Levy
- Department of Genetics, APHP-Robert Debré University Hospital, Paris, France; Laboratoire de biologie médicale multisites Seqoia - FMG2025, Paris, France
| | - Séverine Drunat
- Department of Genetics, APHP-Robert Debré University Hospital, Paris, France; Laboratoire de biologie médicale multisites Seqoia - FMG2025, Paris, France; INSERM UMR1141, Neurodiderot, University of Paris, Paris, France
| | - Marie Vincent
- Service de Génétique Médicale, CHU Nantes, Nantes, France; Inserm, CNRS, University Nantes, l'institut du thorax, Nantes, France
| | - Agnès Guet
- APHP.Nord, Louis Mourier Hospital, Pediatrics Department, Paris, France
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer L Murphy
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - James R Lupski
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Gilbert Vezina
- Department of Diagnostic Radiology and Imaging, Children's National Hospital, Washington, DC, USA
| | - Ellen F Macnamara
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - David R Adams
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maria T Acosta
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia J Tifft
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - William A Gahl
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA; Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - May Christine V Malicdan
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA; Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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6
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Soldatos A, Nutman TB, Johnson T, Dowell SF, Sejvar JJ, Wilson MR, DeRisi JL, Inati SK, Groden C, Evans C, O'Connell EM, Toliva BO, Aceng JR, Aryek-Kwe J, Toro C, Stratakis CA, Buckler AG, Cantilena C, Palmore TN, Thurm A, Baker EH, Chang R, Fauni H, Adams D, Macnamara EF, Lau CC, Malicdan MCV, Pusey-Swerdzewski B, Downing R, Bunga S, Thomas JD, Gahl WA, Nath A. Genomic analysis, immunomodulation and deep phenotyping of patients with nodding syndrome. Brain 2023; 146:968-976. [PMID: 36181424 PMCID: PMC10169415 DOI: 10.1093/brain/awac357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 07/22/2022] [Accepted: 08/03/2022] [Indexed: 11/14/2022] Open
Abstract
The aetiology of nodding syndrome remains unclear, and comprehensive genotyping and phenotyping data from patients remain sparse. Our objectives were to characterize the phenotype of patients with nodding syndrome, investigate potential contributors to disease aetiology, and evaluate response to immunotherapy. This cohort study investigated members of a single-family unit from Lamwo District, Uganda. The participants for this study were selected by the Ugandan Ministry of Health as representative for nodding syndrome and with a conducive family structure for genomic analyses. Of the eight family members who participated in the study at the National Institutes of Health (NIH) Clinical Center, three had nodding syndrome. The three affected patients were extensively evaluated with metagenomic sequencing for infectious pathogens, exome sequencing, spinal fluid immune analyses, neurometabolic and toxicology testing, continuous electroencephalography and neuroimaging. Five unaffected family members underwent a subset of testing for comparison. A distinctive interictal pattern of sleep-activated bursts of generalized and multifocal epileptiform discharges and slowing was observed in two patients. Brain imaging showed two patients had mild generalized cerebral atrophy, and both patients and unaffected family members had excessive metal deposition in the basal ganglia. Trace metal biochemical evaluation was normal. CSF was non-inflammatory and one patient had CSF-restricted oligoclonal bands. Onchocerca volvulus-specific antibodies were present in all patients and skin snips were negative for active onchocerciasis. Metagenomic sequencing of serum and CSF revealed hepatitis B virus in the serum of one patient. Vitamin B6 metabolites were borderline low in all family members and CSF pyridoxine metabolites were normal. Mitochondrial DNA testing was normal. Exome sequencing did not identify potentially causal candidate gene variants. Nodding syndrome is characterized by a distinctive pattern of sleep-activated epileptiform activity. The associated growth stunting may be due to hypothalamic dysfunction. Extensive testing years after disease onset did not clarify a causal aetiology. A trial of immunomodulation (plasmapheresis in two patients and intravenous immunoglobulin in one patient) was given without short-term effect, but longer-term follow-up was not possible to fully assess any benefit of this intervention.
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Affiliation(s)
- Ariane Soldatos
- National Institutes of Health Intramural Research Program, Bethesda, MD 20892, USA
| | - Thomas B Nutman
- National Institutes of Health Intramural Research Program, Bethesda, MD 20892, USA
| | - Tory Johnson
- National Institutes of Health Intramural Research Program, Bethesda, MD 20892, USA
| | - Scott F Dowell
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - James J Sejvar
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Michael R Wilson
- University of California San Francisco, San Francisco, CA 94143, USA.,Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Joseph L DeRisi
- University of California San Francisco, San Francisco, CA 94143, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Sara K Inati
- National Institutes of Health Intramural Research Program, Bethesda, MD 20892, USA
| | - Catherine Groden
- National Institutes of Health Intramural Research Program, Bethesda, MD 20892, USA
| | - Colleen Evans
- National Institutes of Health Intramural Research Program, Bethesda, MD 20892, USA
| | - Elise M O'Connell
- National Institutes of Health Intramural Research Program, Bethesda, MD 20892, USA
| | | | | | | | - Camilo Toro
- National Institutes of Health Intramural Research Program, Bethesda, MD 20892, USA
| | | | - A Gretchen Buckler
- National Institutes of Health Intramural Research Program, Bethesda, MD 20892, USA
| | - Cathy Cantilena
- National Institutes of Health Intramural Research Program, Bethesda, MD 20892, USA
| | - Tara N Palmore
- National Institutes of Health Intramural Research Program, Bethesda, MD 20892, USA
| | - Audrey Thurm
- National Institutes of Health Intramural Research Program, Bethesda, MD 20892, USA
| | - Eva H Baker
- National Institutes of Health Intramural Research Program, Bethesda, MD 20892, USA
| | - Richard Chang
- National Institutes of Health Intramural Research Program, Bethesda, MD 20892, USA
| | - Harper Fauni
- National Institutes of Health Intramural Research Program, Bethesda, MD 20892, USA
| | - David Adams
- National Institutes of Health Intramural Research Program, Bethesda, MD 20892, USA
| | - Ellen F Macnamara
- National Institutes of Health Intramural Research Program, Bethesda, MD 20892, USA
| | - C Christopher Lau
- National Institutes of Health Intramural Research Program, Bethesda, MD 20892, USA
| | | | | | - Robert Downing
- Uganda Virus Research Institute, Ministry of Health, Entebbe, Republic of Uganda
| | - Sudhir Bunga
- Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Jerry D Thomas
- National Center for Environmental Health, Atlanta, GA 30341, USA
| | - William A Gahl
- National Institutes of Health Intramural Research Program, Bethesda, MD 20892, USA
| | - Avindra Nath
- National Institutes of Health Intramural Research Program, Bethesda, MD 20892, USA
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7
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Andrews JC, Mok JW, Kanca O, Jangam S, Tifft C, Macnamara EF, Russell BE, Wang LK, Nelson SF, Bellen HJ, Yamamoto S, Malicdan MCV, Wangler MF. De Novo Variants in MRTFB have gain of function activity in Drosophila and are associated with a novel neurodevelopmental phenotype with dysmorphic features. Genet Med 2023:100833. [PMID: 37013900 DOI: 10.1016/j.gim.2023.100833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023] Open
Abstract
PURPOSE Myocardin-Related Transcription Factor B (MRTFB) is an important transcriptional regulator which promotes the activity of an estimated 300 genes but is not known to underlie a Mendelian disorder. METHODS Probands were identified through the efforts of the Undiagnosed Disease Network. As the MRTFB protein is highly conserved between vertebrate and invertebrate model organisms, we generated a humanized Drosophila model expressing the human MRTFB protein in the same spatial and temporal pattern as the fly gene. Actin binding assays were used to validate the effect of the variants on MRTFB. RESULTS Here we report two pediatric probands with de novo variants in MRTFB (p.R104G and p.A91P) and mild dysmorphic features, intellectual disability, global developmental delays, speech apraxia, and impulse control issues. Expression of the variants within wing tissues of a fruit fly model resulted in changes in wing morphology. The MRTFBR104G and MRTFBA91P variants also display a decreased level of actin binding within critical RPEL domains, resulting in increased transcriptional activity and changes in the organization of the Actin cytoskeleton. CONCLUSION The MRTFBR104G and MRTFBA91P variants affect the regulation of the protein and underlie a novel neurodevelopmental disorder. Overall, our data suggests these variants act as a gain of function.
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8
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Cassini TA, Malicdan MCV, Macnamara EF, Lehky T, Horkayne-Szakaly I, Huang Y, Jones R, Godfrey R, Wolfe L, Gahl WA, Toro C. MYH2-associated myopathy caused by a novel splice-site variant. Neuromuscul Disord 2023; 33:257-262. [PMID: 36774715 PMCID: PMC10023425 DOI: 10.1016/j.nmd.2022.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 12/29/2022]
Abstract
MYH2 encodes MyHCIIa, a myosin heavy chain found in fast type 2A fibers. Pathogenic variants in this gene have previously been implicated in dominant and recessive forms of myopathy. Three individuals reported here are part of a family in which four generations of individuals are affected by a slowly progressive, predominantly proximal myopathy in an autosomal dominant inheritance pattern. Affected individuals in this family lacked classic features of an MYH2-associated myopathy such as congenital contractures and ophthalmoplegia. A novel variant, MYH2 c.5673+1G>C, was detected in the proband and subsequently found to segregate with disease in five additional family members. Further studies demonstrated that this variant affects splicing, resulting in novel transcripts. These data and muscle biopsy findings in the proband, indicate that this family's MYH2 variant is causative of their myopathy, adding to our understanding of the clinical and molecular characteristics of the disease.
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Affiliation(s)
- Thomas A Cassini
- Medical Genetics and Genomic Medicine Training Program, NIH, National Human Genome Research Institute (NHGRI), 9000 Rockville Pike, Bethesda, MD 20892, USA.
| | | | - Ellen F Macnamara
- Common Fund, NIH, NIH Undiagnosed Diseases Program, Bethesda, MD, USA
| | - Tanya Lehky
- EMG Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Yan Huang
- Common Fund, NIH, NIH Undiagnosed Diseases Program, Bethesda, MD, USA
| | - Robert Jones
- The Joint Pathology Center, Defense Health Agency, Silver Spring, MD 20910, USA
| | - Rena Godfrey
- Common Fund, NIH, NIH Undiagnosed Diseases Program, Bethesda, MD, USA
| | - Lynne Wolfe
- Common Fund, NIH, NIH Undiagnosed Diseases Program, Bethesda, MD, USA
| | - William A Gahl
- Common Fund, NIH, NIH Undiagnosed Diseases Program, Bethesda, MD, USA; Office of the Clinical Director, National Human Genome Research Institute (NHGRI), NIH, Bethesda, MD, USA
| | - Camilo Toro
- Common Fund, NIH, NIH Undiagnosed Diseases Program, Bethesda, MD, USA
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9
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Morimoto M, Bhambhani V, Gazzaz N, Davids M, Sathiyaseelan P, Macnamara EF, Lange J, Lehman A, Zerfas PM, Murphy JL, Acosta MT, Wang C, Alderman E, Reichert S, Thurm A, Adams DR, Introne WJ, Gorski SM, Boerkoel CF, Gahl WA, Tifft CJ, Malicdan MCV, Baldridge D, Bale J, Bamshad M, Barbouth D, Bayrak-Toydemir P, Beck A, Beggs AH, Behrens E, Bejerano G, Bellen HJ, Bennett J, Berg-Rood B, Bernstein JA, Berry GT, Bican A, Bivona S, Blue E, Bohnsack J, Bonner D, Botto L, Boyd B, Briere LC, Brokamp E, Brown G, Burke EA, Burrage LC, Butte MJ, Byers P, Byrd WE, Carey J, Carrasquillo O, Cassini T, Chang TCP, Chanprasert S, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Coggins M, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, Crouse AB, Cunningham M, D’Souza P, Dai H, Dasari S, Davis J, Dayal JG, Dell’Angelica EC, Dipple K, Doherty D, Dorrani N, Doss AL, Douine ED, Duncan L, Earl D, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Falk M, Fieg EL, Fisher PG, Fogel BL, Forghani I, Glass I, Gochuico B, Goddard PC, Godfrey RA, Golden-Grant K, Grajewski A, Gutierrez I, Hadley D, Hahn S, Halley MC, Hamid R, Hassey K, Hayes N, High F, Hing A, Hisama FM, Holm IA, Hom J, Horike-Pyne M, Huang A, Hutchison S, Introne WJ, Isasi R, Izumi K, Jamal F, Jarvik GP, Jarvik J, Jayadev S, Jean-Marie O, Jobanputra V, Karaviti L, Kennedy J, Ketkar S, Kiley D, Kilich G, Kobren SN, Kohane IS, Kohler JN, Korrick S, Kozuira M, Krakow D, Krasnewich DM, Kravets E, Lalani SR, Lam B, Lam C, Lanpher BC, Lanza IR, LeBlanc K, Lee BH, Levitt R, Lewis RA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, MacRae CA, Maduro VV, Mahoney R, Mak BC, Mamounas LA, Manolio TA, Mao R, Maravilla K, Marom R, Marth G, Martin BA, Martin MG, Martínez-Agosto JA, Marwaha S, McCauley J, McConkie-Rosell A, McCray AT, McGee E, Mefford H, Merritt JL, Might M, Mirzaa G, Morava E, Moretti P, Nakano-Okuno M, Nelson SF, Newman JH, Nicholas SK, Nickerson D, Nieves-Rodriguez S, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CGS, Papp JC, Parker NH, Phillips JA, Posey JE, Potocki L, Pusey Swerdzewski BN, Quinlan A, Rao DA, Raper A, Raskind W, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rosenwasser N, Rossignol F, Ruzhnikov M, Sacco R, Sampson JB, Saporta M, Schaechter J, Schedl T, Schoch K, Scott DA, Scott CR, Shashi V, Shin J, Silverman EK, Sinsheimer JS, Sisco K, Smith EC, Smith KS, Solem E, Solnica-Krezel L, Solomon B, Spillmann RC, Stoler JM, Sullivan K, Sullivan JA, Sun A, Sutton S, Sweetser DA, Sybert V, Tabor HK, Tan QKG, Tan ALM, Tekin M, Telischi F, Thorson W, Toro C, Tran AA, Ungar RA, Urv TK, Vanderver A, Velinder M, Viskochil D, Vogel TP, Wahl CE, Walker M, Wallace S, Walley NM, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Wegner D, Weisz Hubshman M, Wener M, Wenger T, Wesseling Perry K, Westerfield M, Wheeler MT, Whitlock J, Wolfe LA, Worley K, Xiao C, Yamamoto S, Yang J, Zhang Z, Zuchner S, Reichert S, Thurm A, Adams DR, Introne WJ, Gorski SM, Boerkoel CF, Gahl WA, Tifft CJ, Malicdan MCV. Bi-allelic ATG4D variants are associated with a neurodevelopmental disorder characterized by speech and motor impairment. NPJ Genom Med 2023; 8:4. [PMID: 36765070 PMCID: PMC9918471 DOI: 10.1038/s41525-022-00343-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 12/06/2022] [Indexed: 02/12/2023] Open
Abstract
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.
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Affiliation(s)
- Marie Morimoto
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Vikas Bhambhani
- grid.418506.e0000 0004 0629 5022Department of Medical Genetics, Children’s Hospitals and Clinics of Minnesota, Minneapolis, MN 55404 USA
| | - Nour Gazzaz
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada ,grid.412125.10000 0001 0619 1117Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mariska Davids
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Paalini Sathiyaseelan
- grid.434706.20000 0004 0410 5424Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3 Canada ,grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Ellen F. Macnamara
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | | | - Anna Lehman
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada
| | - Patricia M. Zerfas
- grid.94365.3d0000 0001 2297 5165Diagnostic and Research Services Branch, Office of Research Services, National Institutes of Health, Bethesda, MD 20892 USA
| | - Jennifer L. Murphy
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Maria T. Acosta
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Camille Wang
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Emily Alderman
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada
| | | | - Sara Reichert
- grid.418506.e0000 0004 0629 5022Department of Medical Genetics, Children’s Hospitals and Clinics of Minnesota, Minneapolis, MN 55404 USA
| | - Audrey Thurm
- grid.94365.3d0000 0001 2297 5165Neurodevelopmental and Behavioral Phenotyping Service, Office of the Clinical Director, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892 USA
| | - David R. Adams
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Wendy J. Introne
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Sharon M. Gorski
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.434706.20000 0004 0410 5424Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3 Canada ,grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Cornelius F. Boerkoel
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada
| | - William A. Gahl
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Cynthia J. Tifft
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - May Christine V. Malicdan
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
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Miller IM, Yashar BM, Macnamara EF, Adams DR, Agrawal PB, Alvey J, Amendola L, Andrews A, Ashley EA, Azamian MS, Bacino CA, Bademci G, Baker E, Balasubramanyam A, Baldridge D, Bale J, Bamshad M, Barbouth D, Bayrak-Toydemir P, Beck A, Beggs AH, Behrens E, Bejerano G, Bellen HJ, Bennett J, Berg-Rood B, Bernstein JA, Berry GT, Bican A, Bivona S, Blue E, Bohnsack J, Bonnenmann C, Bonner D, Botto L, Boyd B, Briere LC, Brokamp E, Brown G, Burke EA, Burrage LC, Butte MJ, Byers P, Byrd WE, Carey J, Carrasquillo O, Chang TCP, Chanprasert S, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Coggins M, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, Crouse AB, Cunningham M, D’Souza P, Dai H, Dasari S, Davis J, Dayal JG, Dell’Angelica EC, Dipple K, Doherty D, Dorrani N, Doss AL, Douine ED, Draper DD, Duncan L, Earl D, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Falk M, Fernandez L, Ferreira C, Fieg EL, Findley LC, Fisher PG, Fogel BL, Forghani I, Gahl WA, Glass I, Gochuico B, Godfrey RA, Golden-Grant K, Goldrich MP, Goldstein DB, Grajewski A, Groden CA, Gutierrez I, Hahn S, Hamid R, Hassey K, Hayes N, High F, Hing A, Hisama FM, Holm IA, Hom J, Horike-Pyne M, Huang Y, Huang A, Huryn L, Isasi R, Izumi K, Jamal F, Jarvik GP, Jarvik J, Jayadev S, Karaviti L, Kennedy J, Ketkar S, Kiley D, Kilich G, Kobren SN, Kohane IS, Kohler JN, Korrick S, Kozuira M, Krakow D, Krasnewich DM, Kravets E, Krier JB, Lalani SR, Lam B, Lam C, LaMoure GL, Lanpher BC, Lanza IR, Latham L, LeBlanc K, Lee BH, Lee H, Levitt R, Lewis RA, Lincoln SA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, MacDowall J, Macnamara EF, MacRae CA, Maduro VV, Mahoney R, Mak BC, Malicdan MCV, Mamounas LA, Manolio TA, Mao R, Maravilla K, Markello TC, Marom R, Marth G, Martin BA, Martin MG, Martfnez-Agosto JA, Marwaha S, McCauley J, McConkie-Rosell A, McCray AT, McGee E, Mefford H, Merritt JL, Might M, Mirzaa G, Morava E, Moretti PM, Moretti P, Mosbrook-Davis D, Mulvihill JJ, Nakano-Okuno M, Nath A, Nelson SF, Newman JH, Nicholas SK, Nickerson D, Nieves-Rodriguez S, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CGS, Papp JC, Parker NH, Phillips JA, Posey JE, Potocki L, Power B, Pusey BN, Quinlan A, Raja AN, Rao DA, Raper A, Raskind W, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rosenwasser N, Rossignol F, Ruzhnikov M, Sacco R, Sampson JB, Saporta M, Schaechter J, Schedl T, Schoch K, Scott DA, Scott CR, Shashi V, Shin J, Signer RH, Silverman EK, Sinsheimer JS, Sisco K, Smith EC, Smith KS, Solem E, Solnica-Krezel L, Solomon B, Spillmann RC, Stoler JM, Sullivan K, Sullivan JA, Sun A, Sutton S, Sweetser DA, Sybert V, Tabor HK, Tan QKG, Tan ALM, Tekin M, Telischi F, Thorson W, Thurm A, Tifft CJ, Toro C, Tran AA, Tucker BM, Urv TK, Vanderver A, Velinder M, Viskochil D, Vogel TP, Wahl CE, Walker M, Wallace S, Walley NM, Walsh CA, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Wegner D, Hubshman MW, Wener M, Wenger T, Perry KW, Westerfield M, Wheeler MT, Whitlock J, Wolfe LA, Woods JD, Worley K, Yamamoto S, Yang J, Yousef M, Zastrow DB, Zein W, Zhang Z, Zhao C, Zuchner S, Macnamara EF. Continuing a search for a diagnosis: the impact of adolescence and family dynamics. Orphanet J Rare Dis 2023; 18:6. [PMID: 36624503 PMCID: PMC9830697 DOI: 10.1186/s13023-022-02598-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 12/14/2022] [Indexed: 01/11/2023] Open
Abstract
The "diagnostic odyssey" describes the process those with undiagnosed conditions undergo to identify a diagnosis. Throughout this process, families of children with undiagnosed conditions have multiple opportunities to decide whether to continue or stop their search for a diagnosis and accept the lack of a diagnostic label. Previous studies identified factors motivating a family to begin searching, but there is limited information about the decision-making process in a prolonged search and how the affected child impacts a family's decision. This study aimed to understand how families of children with undiagnosed diseases decide whether to continue to pursue a diagnosis after standard clinical testing has failed. Parents who applied to the Undiagnosed Disease Network (UDN) at the National Institutes of Health (NIH) were recruited to participate in semi-structured interviews. The 2015 Supportive Care Needs model by Pelenstov, which defines critical needs in families with rare/undiagnosed diseases, provided a framework for interview guide development and transcript analysis (Pelentsov et al in Disabil Health J 8(4):475-491, 2015. https://doi.org/10.1016/J.DHJO.2015.03.009 ). A deductive, iterative coding approach was used to identify common unifying themes. Fourteen parents from 13 families were interviewed. The average child's age was 11 years (range 3-18) and an average 63% of their life had been spent searching for a diagnosis. Our analysis found that alignment or misalignment of parent and child needs impact the trajectory of the diagnostic search. When needs and desires align, reevaluation of a decision to pursue a diagnosis is limited. However, when there is conflict between parent and child desires, there is reevaluation, and often a pause, in the search. This tension is exacerbated when children are adolescents and attempting to balance their dependence on parents for medical care with a natural desire for independence. Our results provide novel insights into the roles of adolescents in the diagnostic odyssey. The tension between desired and realistic developmental outcomes for parents and adolescents impacts if, and how, the search for a diagnosis progresses.
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Affiliation(s)
- Ilana M. Miller
- grid.239560.b0000 0004 0482 1586Children’s National Medical Center, Rare Disease Institute, 7125 13th Place NW, DC 20012 Washington, USA ,grid.214458.e0000000086837370Department of Human Genetics, University of Michigan, 4909 Buhl Building, Catherine St, Ann Arbor, MI 48109 USA
| | - Beverly M. Yashar
- grid.214458.e0000000086837370Department of Human Genetics, University of Michigan, 4909 Buhl Building, Catherine St, Ann Arbor, MI 48109 USA
| | | | - Ellen F. Macnamara
- grid.453125.40000 0004 0533 8641National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD USA
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11
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Montano C, Cassini T, Ziegler SG, Boehm M, Nicoli ER, Mindell JA, Soldatos AG, Manoli I, Wolfe L, Macnamara EF, Malicdan MCV, Adams DR, Tifft CJ, Toro C, Gahl WA. Diagnosis and discovery: Insights from the NIH Undiagnosed Diseases Program. J Inherit Metab Dis 2022; 45:907-918. [PMID: 35490291 DOI: 10.1002/jimd.12506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/14/2022] [Accepted: 04/27/2022] [Indexed: 11/11/2022]
Abstract
Living with an undiagnosed medical condition places a tremendous burden on patients, their families, and their healthcare providers. The Undiagnosed Diseases Program (UDP) was established at the National Institutes of Health (NIH) in 2008 with the primary goals of providing a diagnosis for patients with mysterious conditions and advancing medical knowledge about rare and common diseases. The program reviews applications from referring clinicians for cases that are considered undiagnosed despite a thorough evaluation. Those that are accepted receive clinical evaluations involving deep phenotyping and genetic testing that includes exome and genomic sequencing. Selected candidate gene variants are evaluated by collaborators using functional assays. Since its inception, the UDP has received more than 4500 applications and has completed evaluations on nearly 1300 individuals. Here we present six cases that exemplify the discovery of novel disease mechanisms, the importance of deep phenotyping for rare diseases, and how genetic diagnoses have led to appropriate treatment. The creation of the Undiagnosed Diseases Network (UDN) in 2014 has substantially increased the number of patients evaluated and allowed for greater opportunities for data sharing. Expansion to the Undiagnosed Diseases Network International (UDNI) has the possibility to extend this reach even farther. Together, networks of undiagnosed diseases programs are powerful tools to advance our knowledge of pathophysiology, accelerate accurate diagnoses, and improve patient care for patients with rare conditions.
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Affiliation(s)
- Carolina Montano
- Medical Genetics & Genomic Medicine Training Program, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
| | - Thomas Cassini
- Medical Genetics & Genomic Medicine Training Program, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
| | - Shira G Ziegler
- Departments of Pediatrics and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Manfred Boehm
- Laboratory of Cardiovascular Regenerative Medicine, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA
| | - Elena-Raluca Nicoli
- Glycosphingolipid and Glycoprotein Disorders Unit, Medical Genetics Branch, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
| | - Joseph A Mindell
- Membrane Transport Biophysics Section, National Institute of Neurological Disorders and Stroke (NINDS), NIH, Bethesda, Maryland, USA
| | - Ariane G Soldatos
- Office of the Clinical Director, National Institute of Neurological Disorders and Stroke (NINDS), NIH, Bethesda, Maryland, USA
| | - Irini Manoli
- Organic Acid Research Section, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
| | - Lynne Wolfe
- Office of the Clinical Director, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
| | - Ellen F Macnamara
- NIH Undiagnosed Diseases Program, Common Fund, NIH, Bethesda, Maryland, USA
| | | | - David R Adams
- Office of the Clinical Director, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
- NIH Undiagnosed Diseases Program, Common Fund, NIH, Bethesda, Maryland, USA
| | - Cynthia J Tifft
- Glycosphingolipid and Glycoprotein Disorders Unit, Medical Genetics Branch, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
- Office of the Clinical Director, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
- NIH Undiagnosed Diseases Program, Common Fund, NIH, Bethesda, Maryland, USA
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, Common Fund, NIH, Bethesda, Maryland, USA
| | - William A Gahl
- Office of the Clinical Director, National Human Genome Research Institute (NHGRI), NIH, Bethesda, Maryland, USA
- NIH Undiagnosed Diseases Program, Common Fund, NIH, Bethesda, Maryland, USA
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12
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Ferdinandusse S, McWalter K, Te Brinke H, IJlst L, Mooijer PM, Ruiter JPN, van Lint AEM, Pras-Raves M, Wever E, Millan F, Guillen Sacoto MJ, Begtrup A, Tarnopolsky M, Brady L, Ladda RL, Sell SL, Nowak CB, Douglas J, Tian C, Ulm E, Perlman S, Drack AV, Chong K, Martin N, Brault J, Brokamp E, Toro C, Gahl WA, Macnamara EF, Wolfe L, Waisfisz Q, Zwijnenburg PJG, Ziegler A, Barth M, Smith R, Ellingwood S, Gaebler-Spira D, Bakhtiari S, Kruer MC, van Kampen AHC, Wanders RJA, Waterham HR, Cassiman D, Vaz FM. Correction to: An autosomal dominant neurological disorder caused by de novo variants in FAR1 resulting in uncontrolled synthesis of ether lipids. Genet Med 2021; 23:2467. [PMID: 34667295 PMCID: PMC8629751 DOI: 10.1038/s41436-021-01189-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands.
| | | | - Heleen Te Brinke
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Lodewijk IJlst
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Petra M Mooijer
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Jos P N Ruiter
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Alida E M van Lint
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Mia Pras-Raves
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Eric Wever
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | | | | | | | - Mark Tarnopolsky
- Department of Pediatrics, McMaster University Children's Hospital, Hamilton, ON, Canada
| | - Lauren Brady
- Department of Pediatrics, McMaster University Children's Hospital, Hamilton, ON, Canada
| | - Roger L Ladda
- Department of Pediatrics, Penn State Children's Hospital, Hershey, PA, USA
| | - Susan L Sell
- Department of Pediatrics, Penn State Children's Hospital, Hershey, PA, USA
| | - Catherine B Nowak
- The Feingold Center for Children, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Jessica Douglas
- The Feingold Center for Children, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Cuixia Tian
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Elizabeth Ulm
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Seth Perlman
- Department of Neurology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Arlene V Drack
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
| | - Karen Chong
- Mount Sinai Hospital, Department of Obstetrics and Gynecology, Prenatal Diagnosis and Medical Genetics Program, Toronto, ON, Canada
| | - Nicole Martin
- Mount Sinai Hospital, Department of Obstetrics and Gynecology, Prenatal Diagnosis and Medical Genetics Program, Toronto, ON, Canada
| | - Jennifer Brault
- Vanderbilt University Medical Center, Department of Pediatrics, Nashville, TN, USA
| | - Elly Brokamp
- Vanderbilt University Medical Center, Department of Pediatrics, Nashville, TN, USA
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Ellen F Macnamara
- NIH Undiagnosed Diseases Program, Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Lynne Wolfe
- NIH Undiagnosed Diseases Program, Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Quinten Waisfisz
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Petra J G Zwijnenburg
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Alban Ziegler
- Genetic department, University Hospital Angers, Angers, France
| | - Magalie Barth
- Genetic department, University Hospital Angers, Angers, France
| | - Rosemarie Smith
- Division of Genetics, Department of Pediatrics, Maine Medical Center, Portland, ME, USA
| | - Sara Ellingwood
- Division of Genetics, Department of Pediatrics, Maine Medical Center, Portland, ME, USA
| | - Deborah Gaebler-Spira
- Feinberg Northwestern University School of Medicine, Shirley Ryan Ability Lab, Chicago, IL, USA
| | - Somayeh Bakhtiari
- Barrow Neurological Institute, Phoenix Children's Hospital and University of Arizona College of Medicine, Phoenix, AZ, USA
| | - Michael C Kruer
- Barrow Neurological Institute, Phoenix Children's Hospital and University of Arizona College of Medicine, Phoenix, AZ, USA
| | - Antoine H C van Kampen
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - David Cassiman
- Department of Gastroenterology-Hepatology, Metabolic Center, University Hospitals Leuven, Leuven, Belgium
| | - Frédéric M Vaz
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands.
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Sturrock BRH, Macnamara EF, McGuire P, Kruk S, Yang I, Murphy J, Tifft CJ, Gordon‐Lipkin E. Progressive cerebellar atrophy in a patient with complex II and III deficiency and a novel deleterious variant in SDHA: A Counseling Conundrum. Mol Genet Genomic Med 2021; 9:e1692. [PMID: 33960148 PMCID: PMC8222855 DOI: 10.1002/mgg3.1692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 03/08/2021] [Accepted: 03/19/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Complex II is an essential component of the electron transport chain, linking it with the tricarboxylic acid cycle. Its four subunits are encoded in the nuclear genome, and deleterious variants in these genes, including SDHA (OMIM 600857), are associated with a wide range of symptoms including neurological disease, cardiomyopathy, and neoplasia (paraganglioma-pheochromocytomas (PGL/PCC), and gastrointestinal stromal tumors). Deleterious variants of SDHA are most frequently associated with Leigh and Leigh-like syndromes. METHODS AND RESULTS Here, we describe a case of a 9-year-old boy with tremor, nystagmus, hypotonia, developmental delay, significant ataxia, and progressive cerebellar atrophy. He was found to have biallelic variants in SDHA, a known pathogenic variant (c.91C>T (p.R31*)), and a variant of unknown significance (c.454G>A (p.E152K)). Deficient activity of complexes II and III was detected in fibroblasts from the patient consistent with a diagnosis of a respiratory chain disorder. CONCLUSION We, therefore, consider whether c.454G>A (p.E152K) is, indeed, a pathogenic variant, and what implications it has for family members who carry the same variant.
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Affiliation(s)
- Beattie R. H. Sturrock
- National Institutes of Health Undiagnosed Diseases ProgramCommon FundOffice of the DirectorNIHBethesdaMDUSA
- Brighton and Sussex University Hospitals NHS TrustBrightonEngland
| | - Ellen F. Macnamara
- National Institutes of Health Undiagnosed Diseases ProgramCommon FundOffice of the DirectorNIHBethesdaMDUSA
| | - Peter McGuire
- Metabolism, Infection and Immunity SectionNational Human Genome Research InstituteNIHBethesdaMDUSA
| | - Shannon Kruk
- Metabolism, Infection and Immunity SectionNational Human Genome Research InstituteNIHBethesdaMDUSA
| | - Ivan Yang
- Metabolism, Infection and Immunity SectionNational Human Genome Research InstituteNIHBethesdaMDUSA
| | - Jennifer Murphy
- National Institutes of Health Undiagnosed Diseases ProgramCommon FundOffice of the DirectorNIHBethesdaMDUSA
| | - Cyndi J. Tifft
- National Institutes of Health Undiagnosed Diseases ProgramCommon FundOffice of the DirectorNIHBethesdaMDUSA
- Office of the Clinical DirectorNational Human Genome Research InstituteNIHBethesdaMDUSA
| | - Eliza Gordon‐Lipkin
- Metabolism, Infection and Immunity SectionNational Human Genome Research InstituteNIHBethesdaMDUSA
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14
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Ferdinandusse S, McWalter K, Te Brinke H, IJlst L, Mooijer PM, Ruiter JPN, van Lint AEM, Pras-Raves M, Wever E, Millan F, Guillen Sacoto MJ, Begtrup A, Tarnopolsky M, Brady L, Ladda RL, Sell SL, Nowak CB, Douglas J, Tian C, Ulm E, Perlman S, Drack AV, Chong K, Martin N, Brault J, Brokamp E, Toro C, Gahl WA, Macnamara EF, Wolfe L, Waisfisz Q, Zwijnenburg PJG, Ziegler A, Barth M, Smith R, Ellingwood S, Gaebler-Spira D, Bakhtiari S, Kruer MC, van Kampen AHC, Wanders RJA, Waterham HR, Cassiman D, Vaz FM. An autosomal dominant neurological disorder caused by de novo variants in FAR1 resulting in uncontrolled synthesis of ether lipids. Genet Med 2021; 23:740-750. [PMID: 33239752 PMCID: PMC8026396 DOI: 10.1038/s41436-020-01027-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/15/2020] [Accepted: 10/21/2020] [Indexed: 12/25/2022] Open
Abstract
PURPOSE In this study we investigate the disease etiology in 12 patients with de novo variants in FAR1 all resulting in an amino acid change at position 480 (p.Arg480Cys/His/Leu). METHODS Following next-generation sequencing and clinical phenotyping, functional characterization was performed in patients' fibroblasts using FAR1 enzyme analysis, FAR1 immunoblotting/immunofluorescence, and lipidomics. RESULTS All patients had spastic paraparesis and bilateral congenital/juvenile cataracts, in most combined with speech and gross motor developmental delay and truncal hypotonia. FAR1 deficiency caused by biallelic variants results in defective ether lipid synthesis and plasmalogen deficiency. In contrast, patients' fibroblasts with the de novo FAR1 variants showed elevated plasmalogen levels. Further functional studies in fibroblasts showed that these variants cause a disruption of the plasmalogen-dependent feedback regulation of FAR1 protein levels leading to uncontrolled ether lipid production. CONCLUSION Heterozygous de novo variants affecting the Arg480 residue of FAR1 lead to an autosomal dominant disorder with a different disease mechanism than that of recessive FAR1 deficiency and a diametrically opposed biochemical phenotype. Our findings show that for patients with spastic paraparesis and bilateral cataracts, FAR1 should be considered as a candidate gene and added to gene panels for hereditary spastic paraplegia, cerebral palsy, and juvenile cataracts.
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Affiliation(s)
- Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands.
| | | | - Heleen Te Brinke
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Lodewijk IJlst
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Petra M Mooijer
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Jos P N Ruiter
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Alida E M van Lint
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Mia Pras-Raves
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Eric Wever
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | | | | | | | - Mark Tarnopolsky
- Department of Pediatrics, McMaster University Children's Hospital, Hamilton, ON, Canada
| | - Lauren Brady
- Department of Pediatrics, McMaster University Children's Hospital, Hamilton, ON, Canada
| | - Roger L Ladda
- Department of Pediatrics, Penn State Children's Hospital, Hershey, PA, USA
| | - Susan L Sell
- Department of Pediatrics, Penn State Children's Hospital, Hershey, PA, USA
| | - Catherine B Nowak
- The Feingold Center for Children, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Jessica Douglas
- The Feingold Center for Children, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Cuixia Tian
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Elizabeth Ulm
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Seth Perlman
- Department of Neurology, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Arlene V Drack
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA
| | - Karen Chong
- Mount Sinai Hospital, Department of Obstetrics and Gynecology, Prenatal Diagnosis and Medical Genetics Program, Toronto, ON, Canada
| | - Nicole Martin
- Mount Sinai Hospital, Department of Obstetrics and Gynecology, Prenatal Diagnosis and Medical Genetics Program, Toronto, ON, Canada
| | - Jennifer Brault
- Vanderbilt University Medical Center, Department of Pediatrics, Nashville, TN, USA
| | - Elly Brokamp
- Vanderbilt University Medical Center, Department of Pediatrics, Nashville, TN, USA
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Ellen F Macnamara
- NIH Undiagnosed Diseases Program, Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Lynne Wolfe
- NIH Undiagnosed Diseases Program, Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Quinten Waisfisz
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Petra J G Zwijnenburg
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Alban Ziegler
- Genetic department, University Hospital Angers, Angers, France
| | - Magalie Barth
- Genetic department, University Hospital Angers, Angers, France
| | - Rosemarie Smith
- Division of Genetics, Department of Pediatrics, Maine Medical Center, Portland, ME, USA
| | - Sara Ellingwood
- Division of Genetics, Department of Pediatrics, Maine Medical Center, Portland, ME, USA
| | - Deborah Gaebler-Spira
- Feinberg Northwestern University School of Medicine, Shirley Ryan Ability Lab, Chicago, IL, USA
| | - Somayeh Bakhtiari
- Barrow Neurological Institute, Phoenix Children's Hospital and University of Arizona College of Medicine, Phoenix, AZ, USA
| | - Michael C Kruer
- Barrow Neurological Institute, Phoenix Children's Hospital and University of Arizona College of Medicine, Phoenix, AZ, USA
| | - Antoine H C van Kampen
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - David Cassiman
- Department of Gastroenterology-Hepatology, Metabolic Center, University Hospitals Leuven, Leuven, Belgium
| | - Frédéric M Vaz
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands.
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15
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Meissner LE, Macnamara EF, D'Souza P, Yang J, Vezina G, Ferreira CR, Zein WM, Tifft CJ, Adams DR. DYRK1A pathogenic variants in two patients with syndromic intellectual disability and a review of the literature. Mol Genet Genomic Med 2020; 8:e1544. [PMID: 33159716 PMCID: PMC7767569 DOI: 10.1002/mgg3.1544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/24/2020] [Accepted: 10/16/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND DYRK1A-Related Intellectual Disability Syndrome is a rare autosomal dominant condition characterized by intellectual disability, speech and language delays, microcephaly, facial dysmorphism, and feeding difficulties. Affected individuals represent simplex cases that result from de novo heterozygous pathogenic variants in DYRK1A (OMIM 614104), or chromosomal structural rearrangements involving the DYRK1A locus. Due to the rarity of DYRK1A-Related Intellectual Disability Syndrome, the spectrum of symptoms associated with this disease has not been completely defined. METHODS AND RESULTS We present two unrelated cases of DYRK1A-Related Intellectual Disability Syndrome resulting from variants in DYRK1A. Both probands presented to the National Institutes of Health (NIH) with multiple dysmorphic facial features, primary microcephaly, absent or minimal speech, feeding difficulties, and cognitive impairment; features that have been previously reported in individuals with DYRK1A. During NIH evaluation, additional features of enlarged cerebral subarachnoid spaces, retinal vascular tortuosity, and bilateral anomalous large optic discs with increased cup-to-disc ratio were identified in the first proband and multiple ophthalmologic abnormalities and sensorineural hearing loss were identified in the second proband. CONCLUSION We recommend that the workup of future of patients include a comprehensive eye exam. Early establishment of physical, occupational, and speech therapy may help in the management of ataxia, hypertonia, and speech impairments common in these patients.
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Affiliation(s)
- Laura E. Meissner
- Office of the Clinical DirectorNational Human Genome Research InstituteNIHBethesdaMDUSA
- Present address:
Sidney Kimmel Medical College at Thomas Jefferson UniversityPhiladelphiaPAUSA
| | | | - Precilla D'Souza
- Office of the Clinical DirectorNational Human Genome Research InstituteNIHBethesdaMDUSA
- Undiagnosed Diseases ProgramThe Common FundNIHBethesdaMDUSA
| | - John Yang
- Undiagnosed Diseases ProgramThe Common FundNIHBethesdaMDUSA
| | - Gilbert Vezina
- Division of Diagnostic Imaging and RadiologyChildren's National Health SystemWashingtonDCUSA
| | - Carlos R. Ferreira
- Medical Genomics and Metabolic Genetics BranchNational Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Wadih M. Zein
- Ophthalmic Genetics and Visual Function BranchNational Eye InstituteNIHBethesdaMDUSA
| | - Cynthia J. Tifft
- Office of the Clinical DirectorNational Human Genome Research InstituteNIHBethesdaMDUSA
- Undiagnosed Diseases ProgramThe Common FundNIHBethesdaMDUSA
| | - David R. Adams
- Office of the Clinical DirectorNational Human Genome Research InstituteNIHBethesdaMDUSA
- Undiagnosed Diseases ProgramThe Common FundNIHBethesdaMDUSA
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16
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Ferreira CR, Hackbarth ME, Ziegler SG, Pan KS, Roberts MS, Rosing DR, Whelpley MS, Bryant JC, Macnamara EF, Wang S, Müller K, Hartley IR, Chew EY, Corden TE, Jacobsen CM, Holm IA, Rutsch F, Dikoglu E, Chen MY, Mughal MZ, Levine MA, Gafni RI, Gahl WA. Prospective phenotyping of long-term survivors of generalized arterial calcification of infancy (GACI). Genet Med 2020; 23:396-407. [PMID: 33005041 PMCID: PMC7867608 DOI: 10.1038/s41436-020-00983-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 02/07/2023] Open
Abstract
PURPOSE Generalized arterial calcification of infancy (GACI), characterized by vascular calcifications that are often fatal shortly after birth, is usually caused by deficiency of ENPP1. A small fraction of GACI cases result from deficiency of ABCC6, a membrane transporter. The natural history of GACI survivors has not been established in a prospective fashion. METHODS We performed deep phenotyping of 20 GACI survivors. RESULTS Sixteen of 20 subjects presented with arterial calcifications, but only 5 had residual involvement at the time of evaluation. Individuals with ENPP1 deficiency either had hypophosphatemic rickets or were predicted to develop it by 14 years of age; 14/16 had elevated intact FGF23 levels (iFGF23). Blood phosphate levels correlated inversely with iFGF23. For ENPP1-deficient individuals, the lifetime risk of cervical spine fusion was 25%, that of hearing loss was 75%, and the main morbidity in adults was related to enthesis calcification. Four ENPP1-deficient individuals manifested classic skin or retinal findings of PXE. We estimated the minimal incidence of ENPP1 deficiency at ~1 in 200,000 pregnancies. CONCLUSION GACI appears to be more common than previously thought, with an expanding spectrum of overlapping phenotypes. The relationships among decreased ENPP1, increased iFGF23, and rickets could inform future therapies.
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Affiliation(s)
- Carlos R Ferreira
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Mary E Hackbarth
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shira G Ziegler
- Departments of Pediatrics and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kristen S Pan
- Skeletal Disorders and Mineral Homeostasis Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Mary S Roberts
- Skeletal Disorders and Mineral Homeostasis Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Douglas R Rosing
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Margaret S Whelpley
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Joy C Bryant
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ellen F Macnamara
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Iris R Hartley
- Skeletal Disorders and Mineral Homeostasis Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Emily Y Chew
- Division of Epidemiology and Clinical Applications, Clinical Trials Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Timothy E Corden
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Christina M Jacobsen
- Divisions of Endocrinology and Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Ingrid A Holm
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.,Division of Genetics and Genomics and the Manton Center for Orphan Diseases Research, Boston Children's Hospital, Boston, MA, USA
| | - Frank Rutsch
- Department of General Pediatrics, Muenster University Children's Hospital, Muenster, Germany
| | - Esra Dikoglu
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marcus Y Chen
- Cardiovascular CT Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - M Zulf Mughal
- Department of Paediatric Endocrinology, Royal Manchester Children's Hospital, Manchester University Hospital's NHS Trust, Manchester, UK
| | - Michael A Levine
- Division of Endocrinology and Diabetes, The Children's Hospital of Philadelphia and the Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Rachel I Gafni
- Skeletal Disorders and Mineral Homeostasis Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - William A Gahl
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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17
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Abstract
Undiagnosed and rare conditions are collectively common and affect millions of people worldwide. The NIH Undiagnosed Diseases Program (UDP) strives to achieve both a comprehensive diagnosis and a better understanding of the mechanisms of disease for many of these individuals. Through the careful review of records, a well-orchestrated inpatient evaluation, genomic sequencing and testing, and with the use of emerging strategies such as matchmaking programs, the UDP succeeds nearly 30 percent of the time for these highly selective cases. Although the UDP process is built on a unique set of resources, case examples demonstrate steps genetic professionals can take, in both clinical and research settings, to arrive at a diagnosis for their most challenging cases.
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Affiliation(s)
- Ellen F. Macnamara
- National Institutes of Health, Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, MD, USA
| | - Precilla D’Souza
- National Institutes of Health, Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, MD, USA
| | - Undiagnosed Diseases Network
- National Institutes of Health, Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, MD, USA
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia J. Tifft
- National Institutes of Health, Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, MD, USA
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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18
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Mao D, Reuter CM, Ruzhnikov MR, Beck AE, Farrow EG, Emrick LT, Rosenfeld JA, Mackenzie KM, Robak L, Wheeler MT, Burrage LC, Jain M, Liu P, Calame D, Küry S, Sillesen M, Schmitz-Abe K, Tonduti D, Spaccini L, Iascone M, Genetti CA, Koenig MK, Graf M, Tran A, Alejandro M, Lee BH, Thiffault I, Agrawal PB, Bernstein JA, Bellen HJ, Chao HT, Acosta MT, Adam M, Adams DR, Agrawal PB, Alejandro ME, Allard P, Alvey J, Amendola L, Andrews A, Ashley EA, Azamian MS, Bacino CA, Bademci G, Baker E, Balasubramanyam A, Baldridge D, Bale J, Bamshad M, Barbouth D, Batzli GF, Bayrak-Toydemir P, Beck A, Beggs AH, Bejerano G, Bellen HJ, Bennet J, Berg-Rood B, Bernier R, Bernstein JA, Berry GT, Bican A, Bivona S, Blue E, Bohnsack J, Bonnenmann C, Bonner D, Botto L, Briere LC, Brokamp E, Burke EA, Burrage LC, Butte MJ, Byers P, Carey J, Carrasquillo O, Chang TCP, Chanprasert S, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, Cunningham M, D’Souza P, Dai H, Dasari S, Davids M, Dayal JG, Dell’Angelica EC, Dhar SU, Dipple K, Doherty D, Dorrani N, Douine ED, Draper DD, Duncan L, Earl D, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Estwick T, Fernandez L, Ferreira C, Fieg EL, Fisher PG, Fogel BL, Forghani I, Fresard L, Gahl WA, Glass I, Godfrey RA, Golden-Grant K, Goldman AM, Goldstein DB, Grajewski A, Groden CA, Gropman AL, Hahn S, Hamid R, Hanchard NA, Hayes N, High F, Hing A, Hisama FM, Holm IA, Hom J, Horike-Pyne M, Huang A, Huang Y, Isasi R, Jamal F, Jarvik GP, Jarvik J, Jayadev S, Jiang YH, Johnston JM, Karaviti L, Kelley EG, Kiley D, Kohane IS, Kohler JN, Krakow D, Krasnewich DM, Korrick S, Koziura M, Krier JB, Lalani SR, Lam B, Lam C, Lanpher BC, Lanza IR, Lau CC, LeBlanc K, Lee BH, Lee H, Levitt R, Lewis RA, Lincoln SA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Majcherska MM, Malicdan MCV, Mamounas LA, Manolio TA, Mao R, Maravilla K, Markello TC, Marom R, Marth G, Martin BA, Martin MG, Martínez-Agosto JA, Marwaha S, McCauley J, McConkie-Rosell A, McCormack CE, McCray AT, Mefford H, Merritt JL, Might M, Mirzaa G, Morava-Kozicz E, Moretti PM, Morimoto M, Mulvihill JJ, Murdock DR, Nath A, Nelson SF, Newman JH, Nicholas SK, Nickerson D, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CG, Papp JC, Parker NH, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Quinlan A, Raskind W, Raja AN, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rowley RK, Ruzhnikov M, Sacco R, Sampson JB, Samson SL, Saporta M, Scott CR, Schaechter J, Schedl T, Schoch K, Scott DA, Shakachite L, Sharma P, Shashi V, Shin J, Signer R, Sillari CH, Silverman EK, Sinsheimer JS, Sisco K, Smith KS, Solnica-Krezel L, Spillmann RC, Stoler JM, Stong N, Sullivan JA, Sun A, Sutton S, Sweetser DA, Sybert V, Tabor HK, Tamburro CP, Tan QKG, Tekin M, Telischi F, Thorson W, Tifft CJ, Toro C, Tran AA, Urv TK, Velinder M, Viskochil D, Vogel TP, Wahl CE, Wallace S, Walley NM, Walsh CA, Walker M, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Wegner D, Wener M, Westerfield M, Wheeler MT, Wise AL, Wolfe LA, Woods JD, Yamamoto S, Yang J, Yoon AJ, Yu G, Zastrow DB, Zhao C, Zuchner S. De novo EIF2AK1 and EIF2AK2 Variants Are Associated with Developmental Delay, Leukoencephalopathy, and Neurologic Decompensation. Am J Hum Genet 2020; 106:570-583. [PMID: 32197074 PMCID: PMC7118694 DOI: 10.1016/j.ajhg.2020.02.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/28/2020] [Indexed: 02/03/2023] Open
Abstract
EIF2AK1 and EIF2AK2 encode members of the eukaryotic translation initiation factor 2 alpha kinase (EIF2AK) family that inhibits protein synthesis in response to physiologic stress conditions. EIF2AK2 is also involved in innate immune response and the regulation of signal transduction, apoptosis, cell proliferation, and differentiation. Despite these findings, human disorders associated with deleterious variants in EIF2AK1 and EIF2AK2 have not been reported. Here, we describe the identification of nine unrelated individuals with heterozygous de novo missense variants in EIF2AK1 (1/9) or EIF2AK2 (8/9). Features seen in these nine individuals include white matter alterations (9/9), developmental delay (9/9), impaired language (9/9), cognitive impairment (8/9), ataxia (6/9), dysarthria in probands with verbal ability (6/9), hypotonia (7/9), hypertonia (6/9), and involuntary movements (3/9). Individuals with EIF2AK2 variants also exhibit neurological regression in the setting of febrile illness or infection. We use mammalian cell lines and proband-derived fibroblasts to further confirm the pathogenicity of variants in these genes and found reduced kinase activity. EIF2AKs phosphorylate eukaryotic translation initiation factor 2 subunit 1 (EIF2S1, also known as EIF2α), which then inhibits EIF2B activity. Deleterious variants in genes encoding EIF2B proteins cause childhood ataxia with central nervous system hypomyelination/vanishing white matter (CACH/VWM), a leukodystrophy characterized by neurologic regression in the setting of febrile illness and other stressors. Our findings indicate that EIF2AK2 missense variants cause a neurodevelopmental syndrome that may share phenotypic and pathogenic mechanisms with CACH/VWM.
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19
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Macnamara EF, Koehler AE, D'Souza P, Estwick T, Lee P, Vezina G, Fauni H, Braddock SR, Torti E, Holt JM, Sharma P, Malicdan MCV, Tifft CJ. Kilquist syndrome: A novel syndromic hearing loss disorder caused by homozygous deletion of SLC12A2. Hum Mutat 2019; 40:532-538. [PMID: 30740830 DOI: 10.1002/humu.23722] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 01/22/2019] [Accepted: 02/07/2019] [Indexed: 11/07/2022]
Abstract
Syndromic sensorineural hearing loss is multigenic and associated with malformations of the ear and other organ systems. Herein we describe a child admitted to the NIH Undiagnosed Diseases Program with global developmental delay, sensorineural hearing loss, gastrointestinal abnormalities, and absent salivation. Next-generation sequencing revealed a uniparental isodisomy in chromosome 5, and a 22 kb homozygous deletion in SLC12A2, which encodes for sodium, potassium, and chloride transporter in the basolateral membrane of secretory epithelia. Functional studies using patient-derived fibroblasts showed truncated SLC12A2 transcripts and markedly reduced protein abundance when compared with control. Loss of Slc12a2 in mice has been shown to lead to deafness, abnormal neuronal growth and migration, severe gastrointestinal abnormalities, and absent salivation. Together with the described phenotype of the Slc12a2-knockout mouse model, our results suggest that the absence of functional SLC12A2 causes a new genetic syndrome and is crucial for the development of auditory, neurologic, and gastrointestinal tissues.
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Affiliation(s)
- Ellen F Macnamara
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, Maryland.,Office of the Clinical Director, National Human Genome Research Institute National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Alanna E Koehler
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, Maryland
| | - Precilla D'Souza
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, Maryland.,Office of the Clinical Director, National Human Genome Research Institute National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Tyra Estwick
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, Maryland.,Office of the Clinical Director, National Human Genome Research Institute National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Paul Lee
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, Maryland.,Office of the Clinical Director, National Human Genome Research Institute National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Gilbert Vezina
- Division of Diagnostic Imaging and Radiology, Children's National Health System, Washington, District of Columbia
| | -
- Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - Harper Fauni
- Common Fund, Office of the Director, National Institutes of Health, Bethesda, Maryland
| | - Stephen R Braddock
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, Maryland
| | - Erin Torti
- Department of Pediatrics, Saint Louis University School of Medicine, St. Louis, Missouri
| | - James Matthew Holt
- Department of Pediatrics, Saint Louis University School of Medicine, St. Louis, Missouri
| | - Prashant Sharma
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | - May Christine V Malicdan
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, Maryland
| | - Cynthia J Tifft
- National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, Bethesda, Maryland.,Office of the Clinical Director, National Human Genome Research Institute National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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20
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Macnamara EF, Schoch K, Kelley EG, Fieg E, Brokamp E, Signer R, LeBlanc K, McConkie-Rosell A, Palmer CGS. Cases from the Undiagnosed Diseases Network: The continued value of counseling skills in a new genomic era. J Genet Couns 2019; 28:194-201. [PMID: 30680851 DOI: 10.1002/jgc4.1091] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 12/14/2018] [Accepted: 12/16/2018] [Indexed: 01/15/2023]
Abstract
The "diagnostic odyssey" is well known and described in genetic counseling literature. Studies addressing the psychological, emotional, and financial costs of not having a diagnosis have shown how it permeates the lives of patients and families. The Undiagnosed Diseases Network aims to end this odyssey by providing diagnoses to individuals with undiagnosed conditions through multidisciplinary evaluations, whole exome and genome sequencing, and basic science research. It also provides an opportunity to learn from patients and families and to better understand their journeys and the impact of receiving a diagnosis. Seven cases are presented that outline challenges that come from working with chronically undiagnosed and newly diagnosed patients in a time when sequencing for clinical diagnosis is rapidly increasing. They illuminate the emotional journey of patients and families searching for a diagnosis and the mental health problems, financial distress, and chaos that can accompany not having answers. They also illustrate the surprising reactions patients and families can have to receiving a diagnosis, including anger, grief, and disappointment. While the lessons learned from these families are not novel, new strategies are presented for handling these challenges in undiagnosed and ultra-rare populations, groups that will increase with the rise of clinical sequencing.
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Affiliation(s)
- Ellen F Macnamara
- National Institutes of Health, Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, Maryland
| | - Kelly Schoch
- Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina
| | - Emily G Kelley
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Elizabeth Fieg
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts
| | - Elly Brokamp
- Division of Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Rebecca Signer
- Department of Human Genetics, University of California, Los Angeles, California
| | - Kimberly LeBlanc
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Allyn McConkie-Rosell
- Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina
| | - Christina G S Palmer
- Department of Human Genetics, University of California, Los Angeles, California.,Department of Psychiatry & Biobehavioral Sciences, University of California, Los Angeles, California.,Institute for Society and Genetics, University of California, Los Angeles, California
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21
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Machol K, Rousseau J, Ehresmann S, Garcia T, Nguyen TTM, Spillmann RC, Sullivan JA, Shashi V, Jiang YH, Stong N, Fiala E, Willing M, Pfundt R, Kleefstra T, Cho MT, McLaughlin H, Rosello Piera M, Orellana C, Martínez F, Caro-Llopis A, Monfort S, Roscioli T, Nixon CY, Buckley MF, Turner A, Jones WD, van Hasselt PM, Hofstede FC, van Gassen KL, Brooks AS, van Slegtenhorst MA, Lachlan K, Sebastian J, Madan-Khetarpal S, Sonal D, Sakkubai N, Thevenon J, Faivre L, Maurel A, Petrovski S, Krantz ID, Tarpinian JM, Rosenfeld JA, Lee BH, Campeau PM, Adams DR, Alejandro ME, Allard P, Azamian MS, Bacino CA, Balasubramanyam A, Barseghyan H, Batzli GF, Beggs AH, Behnam B, Bican A, Bick DP, Birch CL, Bonner D, Boone BE, Bostwick BL, Briere LC, Brown DM, Brush M, Burke EA, Burrage LC, Chen S, Clark GD, Coakley TR, Cogan JD, Cooper CM, Cope H, Craigen WJ, D’Souza P, Davids M, Dayal JG, Dell’Angelica EC, Dhar SU, Dillon A, Dipple KM, Donnell-Fink LA, Dorrani N, Dorset DC, Douine ED, Draper DD, Eckstein DJ, Emrick LT, Eng CM, Eskin A, Esteves C, Estwick T, Ferreira C, Fogel BL, Friedman ND, Gahl WA, Glanton E, Godfrey RA, Goldstein DB, Gould SE, Gourdine JPF, Groden CA, Gropman AL, Haendel M, Hamid R, Hanchard NA, Handley LH, Herzog MR, Holm IA, Hom J, Howerton EM, Huang Y, Jacob HJ, Jain M, Jiang YH, Johnston JM, Jones AL, Kohane IS, Krasnewich DM, Krieg EL, Krier JB, Lalani SR, Lau CC, Lazar J, Lee BH, Lee H, Levy SE, Lewis RA, Lincoln SA, Lipson A, Loo SK, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Majcherska MM, Malicdan MCV, Mamounas LA, Manolio TA, Markello TC, Marom R, Martínez-Agosto JA, Marwaha S, May T, McConkie-Rosell A, McCormack CE, McCray AT, Might M, Moretti PM, Morimoto M, Mulvihill JJ, Murphy JL, Muzny DM, Nehrebecky ME, Nelson SF, Newberry JS, Newman JH, Nicholas SK, Novacic D, Orange JS, Pallais JC, Palmer CG, Papp JC, Parker NH, Pena LD, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Reuter CM, Robertson AK, Rodan LH, Rosenfeld JA, Sampson JB, Samson SL, Schoch K, Schroeder MC, Scott DA, Sharma P, Shashi V, Signer R, Silverman EK, Sinsheimer JS, Smith KS, Spillmann RC, Splinter K, Stoler JM, Stong N, Sullivan JA, Sweetser DA, Tifft CJ, Toro C, Tran AA, Urv TK, Valivullah ZM, Vilain E, Vogel TP, Wahl CE, Walley NM, Walsh CA, Ward PA, Waters KM, Westerfield M, Wise AL, Wolfe LA, Worthey EA, Yamamoto S, Yang Y, Yu G, Zastrow DB, Zheng A. Expanding the Spectrum of BAF-Related Disorders: De Novo Variants in SMARCC2 Cause a Syndrome with Intellectual Disability and Developmental Delay. Am J Hum Genet 2019; 104:164-178. [PMID: 30580808 DOI: 10.1016/j.ajhg.2018.11.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 11/14/2018] [Indexed: 12/22/2022] Open
Abstract
SMARCC2 (BAF170) is one of the invariable core subunits of the ATP-dependent chromatin remodeling BAF (BRG1-associated factor) complex and plays a crucial role in embryogenesis and corticogenesis. Pathogenic variants in genes encoding other components of the BAF complex have been associated with intellectual disability syndromes. Despite its significant biological role, variants in SMARCC2 have not been directly associated with human disease previously. Using whole-exome sequencing and a web-based gene-matching program, we identified 15 individuals with variable degrees of neurodevelopmental delay and growth retardation harboring one of 13 heterozygous variants in SMARCC2, most of them novel and proven de novo. The clinical presentation overlaps with intellectual disability syndromes associated with other BAF subunits, such as Coffin-Siris and Nicolaides-Baraitser syndromes and includes prominent speech impairment, hypotonia, feeding difficulties, behavioral abnormalities, and dysmorphic features such as hypertrichosis, thick eyebrows, thin upper lip vermilion, and upturned nose. Nine out of the fifteen individuals harbor variants in the highly conserved SMARCC2 DNA-interacting domains (SANT and SWIRM) and present with a more severe phenotype. Two of these individuals present cardiac abnormalities. Transcriptomic analysis of fibroblasts from affected individuals highlights a group of differentially expressed genes with possible roles in regulation of neuronal development and function, namely H19, SCRG1, RELN, and CACNB4. Our findings suggest a novel SMARCC2-related syndrome that overlaps with neurodevelopmental disorders associated with variants in BAF-complex subunits.
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Marcogliese PC, Shashi V, Spillmann RC, Stong N, Rosenfeld JA, Koenig MK, Martínez-Agosto JA, Herzog M, Chen AH, Dickson PI, Lin HJ, Vera MU, Salamon N, Graham JM, Ortiz D, Infante E, Steyaert W, Dermaut B, Poppe B, Chung HL, Zuo Z, Lee PT, Kanca O, Xia F, Yang Y, Smith EC, Jasien J, Kansagra S, Spiridigliozzi G, El-Dairi M, Lark R, Riley K, Koeberl DD, Golden-Grant K, Yamamoto S, Wangler MF, Mirzaa G, Hemelsoet D, Lee B, Nelson SF, Goldstein DB, Bellen HJ, Pena LD, Callens S, Coucke P, Dermaut B, Hemelsoet D, Poppe B, Steyaert W, Terryn W, Van Coster R, Adams DR, Alejandro ME, Allard P, Azamian MS, Bacino CA, Balasubramanyam A, Barseghyan H, Batzli GF, Beggs AH, Behnam B, Bican A, Bick DP, Birch CL, Bonner D, Boone BE, Bostwick BL, Briere LC, Brown DM, Brush M, Burke EA, Burrage LC, Chen S, Clark GD, Coakley TR, Cogan JD, Cooper CM, Cope H, Craigen WJ, D’Souza P, Davids M, Dayal JG, Dell’Angelica EC, Dhar SU, Dillon A, Dipple KM, Donnell-Fink LA, Dorrani N, Dorset DC, Douine ED, Draper DD, Eckstein DJ, Emrick LT, Eng CM, Eskin A, Esteves C, Estwick T, Ferreira C, Fogel BL, Friedman ND, Gahl WA, Glanton E, Godfrey RA, Goldstein DB, Gould SE, Gourdine JPF, Groden CA, Gropman AL, Haendel M, Hamid R, Hanchard NA, Handley LH, Herzog MR, Holm IA, Hom J, Howerton EM, Huang Y, Jacob HJ, Jain M, Jiang YH, Johnston JM, Jones AL, Kohane IS, Krasnewich DM, Krieg EL, Krier JB, Lalani SR, Lau CC, Lazar J, Lee BH, Lee H, Levy SE, Lewis RA, Lincoln SA, Lipson A, Loo SK, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Majcherska MM, Malicdan MCV, Mamounas LA, Manolio TA, Markello TC, Marom R, Martínez-Agosto JA, Marwaha S, May T, McConkie-Rosell A, McCormack CE, McCray AT, Might M, Moretti PM, Morimoto M, Mulvihill JJ, Murphy JL, Muzny DM, Nehrebecky ME, Nelson SF, Newberry JS, Newman JH, Nicholas SK, Novacic D, Orange JS, Pallais JC, Palmer CG, Papp JC, Parker NH, Pena LD, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Reuter CM, Robertson AK, Rodan LH, Rosenfeld JA, Sampson JB, Samson SL, Schoch K, Schroeder MC, Scott DA, Sharma P, Shashi V, Signer R, Silverman EK, Sinsheimer JS, Smith KS, Spillmann RC, Splinter K, Stoler JM, Stong N, Sullivan JA, Sweetser DA, Tifft CJ, Toro C, Tran AA, Urv TK, Valivullah ZM, Vilain E, Vogel TP, Wahl CE, Walley NM, Walsh CA, Ward PA, Waters KM, Westerfield M, Wise AL, Wolfe LA, Worthey EA, Yamamoto S, Yang Y, Yu G, Zastrow DB, Zheng A. IRF2BPL Is Associated with Neurological Phenotypes. Am J Hum Genet 2018; 103:456. [PMID: 30193138 PMCID: PMC6128320 DOI: 10.1016/j.ajhg.2018.08.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Hardee I, Soldatos A, Davids M, Vilboux T, Toro C, David KL, Ferreira CR, Nehrebecky M, Snow J, Thurm A, Heller T, Macnamara EF, Gunay-Aygun M, Zein WM, Gahl WA, Malicdan MCV. Cover Image, Volume 173A, Number 12, December 2017. Am J Med Genet A 2017; 173:i. [PMID: 29136352 DOI: 10.1002/ajmg.a.38548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The cover image, by Isabel Hardee et al., is based on the Clinical Report Defective ciliogenesis in INPP5E-related Joubert syndrome, DOI: 10.1002/ajmg.a.38376. Design Credit: Darryl Leja.
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Affiliation(s)
- Isabel Hardee
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Ariane Soldatos
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Mariska Davids
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Thierry Vilboux
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Department of Medical Genetics, Inova Translational Medicine Institute, Falls Church, Virginia
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | | | - Carlos R Ferreira
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Michele Nehrebecky
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Joseph Snow
- Office of the Clinical Director, National Institute of Mental health, National Institutes of Health, Bethesda, Maryland
| | - Audrey Thurm
- Office of the Clinical Director, National Institute of Mental health, National Institutes of Health, Bethesda, Maryland
| | - Theo Heller
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland
| | - Ellen F Macnamara
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Meral Gunay-Aygun
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Department of Pediatrics and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Wadih M Zein
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - May Christine V Malicdan
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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Hardee I, Soldatos A, Davids M, Vilboux T, Toro C, David KL, Ferreira CR, Nehrebecky M, Snow J, Thurm A, Heller T, Macnamara EF, Gunay-Aygun M, Zein WM, Gahl WA, Malicdan MCV. Defective ciliogenesis in INPP5E-related Joubert syndrome. Am J Med Genet A 2017; 173:3231-3237. [PMID: 29052317 DOI: 10.1002/ajmg.a.38376] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 05/15/2017] [Accepted: 07/01/2017] [Indexed: 12/18/2022]
Abstract
Joubert syndrome is a neurodevelopmental disorder, characterized by malformation of the mid and hindbrain leading to the pathognomonic molar tooth appearance of the brainstem and cerebellum on axial MRI. Core clinical manifestations include hypotonia, tachypnea/apnea, ataxia, ocular motor apraxia, and developmental delay of varying degrees. In addition, a subset of patients has retinal dystrophy, chorioretinal colobomas, hepatorenal fibrocystic disease, and polydactyly. Joubert syndrome exhibits genetic heterogeneity, with mutations identified in more than 30 genes, including INPP5E, a gene encoding inositol polyphosphate 5-phosphatase E, which is important in the development and stability of the primary cilium. Here, we report the detailed clinical phenotypes of two sisters with a novel homozygous variant in INPP5E (NM_019892.4: c.1565G>C, NP_063945.2: p.Gly552Ala), expanding the phenotype associated with Joubert syndrome type 1. Expression studies using patient-derived fibroblasts showed changes in mRNA and protein levels. Analysis of fibroblasts from patients revealed that a significant number of cells had shorter or no cilia, indicating defects in ciliogenesis, and cilia maintenance.
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Affiliation(s)
- Isabel Hardee
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Ariane Soldatos
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Mariska Davids
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Thierry Vilboux
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Department of Medical Genetics, Inova Translational Medicine Institute, Falls Church, Virginia
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | | | - Carlos R Ferreira
- Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Michele Nehrebecky
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Joseph Snow
- Office of the Clinical Director, National Institute of Mental health, National Institutes of Health, Bethesda, Maryland
| | - Audrey Thurm
- Office of the Clinical Director, National Institute of Mental health, National Institutes of Health, Bethesda, Maryland
| | - Theo Heller
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, Maryland
| | - Ellen F Macnamara
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Meral Gunay-Aygun
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Department of Pediatrics and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Wadih M Zein
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - May Christine V Malicdan
- NIH Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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Chao HT, Davids M, Burke E, Pappas JG, Rosenfeld JA, McCarty AJ, Davis T, Wolfe L, Toro C, Tifft C, Xia F, Stong N, Johnson TK, Warr CG, Yamamoto S, Adams DR, Markello TC, Gahl WA, Bellen HJ, Wangler MF, Malicdan MCV, Adams DR, Adams CJ, Alejandro ME, Allard P, Ashley EA, Bacino CA, Balasubramanyam A, Barseghyan H, Beggs AH, Bellen HJ, Bernstein JA, Bick DP, Birch CL, Boone BE, Briere LC, Brown DM, Brush M, Burrage LC, Chao KR, Clark GD, Cogan JD, Cooper CM, Craigen WJ, Davids M, Dayal JG, Dell'Angelica EC, Dhar SU, Dipple KM, Donnell-Fink LA, Dorrani N, Dorset DC, Draper DD, Dries AM, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Estwick T, Fisher PG, Frisby TS, Frost K, Gahl WA, Gartner V, Godfrey RA, Goheen M, Golas GA, Goldstein DB, Gordon M“GG, Gould SE, Gourdine JPF, Graham BH, Groden CA, Gropman AL, Hackbarth ME, Haendel M, Hamid R, Hanchard NA, Handley LH, Hardee I, Herzog MR, Holm IA, Howerton EM, Jacob HJ, Jain M, Jiang YH, Johnston JM, Jones AL, Koehler AE, Koeller DM, Kohane IS, Kohler JN, Krasnewich DM, Krieg EL, Krier JB, Kyle JE, Lalani SR, Latham L, Latour YL, Lau CC, Lazar J, Lee BH, Lee H, Lee PR, Levy SE, Levy DJ, Lewis RA, Liebendorder AP, Lincoln SA, Loomis CR, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Malicdan MCV, Mamounas LA, Manolio TA, Markello TC, Mashid AS, Mazur P, McCarty AJ, McConkie-Rosell A, McCray AT, Metz TO, Might M, Moretti PM, Mulvihill JJ, Murphy JL, Muzny DM, Nehrebecky ME, Nelson SF, Newberry JS, Newman JH, Nicholas SK, Novacic D, Orange JS, Pallais JC, Palmer CG, Papp JC, Pena LD, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Ramoni RB, Rodan LH, Sadozai S, Schaffer KE, Schoch K, Schroeder MC, Scott DA, Sharma P, Shashi V, Silverman EK, Sinsheimer JS, Soldatos AG, Spillmann RC, Splinter K, Stoler JM, Stong N, Strong KA, Sullivan JA, Sweetser DA, Thomas SP, Tift CJ, Tolman NJ, Toro C, Tran AA, Valivullah ZM, Vilain E, Waggott DM, Wahl CE, Walley NM, Walsh CA, Wangler MF, Warburton M, Ward PA, Waters KM, Webb-Robertson BJM, Weech AA, Westerfield M, Wheeler MT, Wise AL, Worthe LA, Worthey EA, Yamamoto S, Yang Y, Yu G, Zornio PA. A Syndromic Neurodevelopmental Disorder Caused by De Novo Variants in EBF3. Am J Hum Genet 2017; 100:128-137. [PMID: 28017372 PMCID: PMC5223093 DOI: 10.1016/j.ajhg.2016.11.018] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/21/2016] [Indexed: 02/06/2023] Open
Abstract
Early B cell factor 3 (EBF3) is a member of the highly evolutionarily conserved Collier/Olf/EBF (COE) family of transcription factors. Prior studies on invertebrate and vertebrate animals have shown that EBF3 homologs are essential for survival and that loss-of-function mutations are associated with a range of nervous system developmental defects, including perturbation of neuronal development and migration. Interestingly, aristaless-related homeobox (ARX), a homeobox-containing transcription factor critical for the regulation of nervous system development, transcriptionally represses EBF3 expression. However, human neurodevelopmental disorders related to EBF3 have not been reported. Here, we describe three individuals who are affected by global developmental delay, intellectual disability, and expressive speech disorder and carry de novo variants in EBF3. Associated features seen in these individuals include congenital hypotonia, structural CNS malformations, ataxia, and genitourinary abnormalities. The de novo variants affect a single conserved residue in a zinc finger motif crucial for DNA binding and are deleterious in a fly model. Our findings indicate that mutations in EBF3 cause a genetic neurodevelopmental syndrome and suggest that loss of EBF3 function might mediate a subset of neurologic phenotypes shared by ARX-related disorders, including intellectual disability, abnormal genitalia, and structural CNS malformations.
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Shashi V, Pena LD, Kim K, Burton B, Hempel M, Schoch K, Walkiewicz M, McLaughlin HM, Cho M, Stong N, Hickey SE, Shuss CM, Freemark MS, Bellet JS, Keels MA, Bonner MJ, El-Dairi M, Butler M, Kranz PG, Stumpel CT, Klinkenberg S, Oberndorff K, Alawi M, Santer R, Petrovski S, Kuismin O, Korpi-Heikkilä S, Pietilainen O, Aarno P, Kurki MI, Hoischen A, Need AC, Goldstein DB, Kortüm F, Bacino A, Lee BH, Balasubramanyam A, Burrage LC, Clark GD, Craigen WJ, Dhar SU, Emrick LT, Graham BH, Jain M, Lalani SR, Lewis RA, Moretti PM, Nicholas SK, Orange JS, Posey JE, Potocki L, Rosenfeld JA, Scott DA, Hanchard NA, Alyssa TA, Mercedes AE, Mashid AS, Bellen HJ, Yamamoto S, Wangler MF, Westerfield M, Postlethwait JH, Eng CM, Yang Y, Muzny DM, Ward PA, Ramoni RB, McCray AT, Kohane IS, Holm IA, Might M, Mazur P, Splinter K, Esteves C, Shashi V, Jiang YH, Pena LD, McConkie-Rosell A, Schoch K, Spillmann RC, Sullivan JA, Walley NM, Goldstein DB, Stong N, Beggs AH, Loscalzo J, MacRae CA, Silverman EK, Stoler JM, Sweetser DA, Maas RL, Krier JB, Rodan LH, Walsh CA, Cooper CM, Pallais JC, Donnell-Fink LA, Krieg EL, Lincoln SA, Briere LC, Jacob HJ, Worthey EA, Lazar J, Strong KA, Handley LH, Newberry JS, Bick DP, Schroeder MC, Brown DM, Birch CL, Levy SE, Boone BE, Dorset DC, Jones AL, Manolio TA, Mulvihill JJ, Wise AL, Dayal JG, Eckstein DJ, Krasnewich DM, Loomis CR, Mamounas LA, Iglesias B, Martin C, Koeller DM, Metz TO, Ashley EA, Fisher PG, Bernstein JA, Wheeler MT, Zornio PA, Waggott DM, Dries AM, Kohler JN, Dipple KM, Nelson SF, Palmer CG, Vilain E, Allard P, Dell Angelica EC, Lee H, Sinsheimer JS, Papp JC, Dorrani N, Herzog MR, Barseghyan H, Adams DR, Adams CJ, Burke EA, Chao KR, Davids M, Draper DD, Estwick T, Frisby TS, Frost K, Gahl WA, Gartner V, Godfrey RA, Goheen M, Golas GA, Gordon MG, Groden CA, Gropman AL, Hackbarth ME, Hardee I, Johnston JM, Koehler AE, Latham L, Latour YL, Lau CYC, Lee PR, Levy DJ, Liebendorder AP, Macnamara EF, Maduro VV, Malicdan MV, Markello TC, McCarty AJ, Murphy JL, Nehrebecky ME, Novacic D, Pusey BN, Sadozai S, Schaffer KE, Sharma P, Soldatos AG, Thomas SP, Tifft CJ, Tolman NJ, Toro C, Valivullah ZM, Wahl CE, Warburton M, Weech AA, Wolfe LA, Yu G, Hamid R, Newman JH, Phillips JA, Cogan JD. De Novo Truncating Variants in ASXL2 Are Associated with a Unique and Recognizable Clinical Phenotype. Am J Hum Genet 2016; 99:991-999. [PMID: 27693232 PMCID: PMC5065681 DOI: 10.1016/j.ajhg.2016.08.017] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 08/24/2016] [Indexed: 12/14/2022] Open
Abstract
The ASXL genes (ASXL1, ASXL2, and ASXL3) participate in body patterning during embryogenesis and encode proteins involved in epigenetic regulation and assembly of transcription factors to specific genomic loci. Germline de novo truncating variants in ASXL1 and ASXL3 have been respectively implicated in causing Bohring-Opitz and Bainbridge-Ropers syndromes, which result in overlapping features of severe intellectual disability and dysmorphic features. ASXL2 has not yet been associated with a human Mendelian disorder. In this study, we performed whole-exome sequencing in six unrelated probands with developmental delay, macrocephaly, and dysmorphic features. All six had de novo truncating variants in ASXL2. A careful review enabled the recognition of a specific phenotype consisting of macrocephaly, prominent eyes, arched eyebrows, hypertelorism, a glabellar nevus flammeus, neonatal feeding difficulties, hypotonia, and developmental disabilities. Although overlapping features with Bohring-Opitz and Bainbridge-Ropers syndromes exist, features that distinguish the ASXL2-associated condition from ASXL1- and ASXL3-related disorders are macrocephaly, absence of growth retardation, and more variability in the degree of intellectual disabilities. We were also able to demonstrate with mRNA studies that these variants are likely to exert a dominant-negative effect, given that both alleles are expressed in blood and the mutated ASXL2 transcripts escape nonsense-mediated decay. In conclusion, de novo truncating variants in ASXL2 underlie a neurodevelopmental syndrome with a clinically recognizable phenotype. This report expands the germline disorders that are linked to the ASXL genes.
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