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Shao DD, Straussberg R, Ahmed H, Khan A, Tian S, Hill RS, Smith RS, Majmundar AJ, Ameziane N, Neil JE, Yang E, Al Tenaiji A, Jamuar SS, Schlaeger TM, Al-Saffar M, Hovel I, Al-Shamsi A, Basel-Salmon L, Amir AZ, Rento LM, Lim JY, Ganesan I, Shril S, Evrony G, Barkovich AJ, Bauer P, Hildebrandt F, Dong M, Borck G, Beetz C, Al-Gazali L, Eyaid W, Walsh CA. A recurrent, homozygous EMC10 frameshift variant is associated with a syndrome of developmental delay with variable seizures and dysmorphic features. Genet Med 2021; 23:1158-1162. [PMID: 33531666 PMCID: PMC8187145 DOI: 10.1038/s41436-021-01097-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 12/28/2020] [Accepted: 01/04/2021] [Indexed: 01/10/2023] Open
Abstract
PURPOSE The endoplasmic reticulum membrane complex (EMC) is a highly conserved, multifunctional 10-protein complex related to membrane protein biology. In seven families, we identified 13 individuals with highly overlapping phenotypes who harbor a single identical homozygous frameshift variant in EMC10. METHODS Using exome, genome, and Sanger sequencing, a recurrent frameshift EMC10 variant was identified in affected individuals in an international cohort of consanguineous families. Multiple families were independently identified and connected via Matchmaker Exchange and internal databases. We assessed the effect of the frameshift variant on EMC10 RNA and protein expression and evaluated EMC10 expression in normal human brain tissue using immunohistochemistry. RESULTS A homozygous variant EMC10 c.287delG (Refseq NM_206538.3, p.Gly96Alafs*9) segregated with affected individuals in each family, who exhibited a phenotypic spectrum of intellectual disability (ID) and global developmental delay (GDD), variable seizures and variable dysmorphic features (elongated face, curly hair, cubitus valgus, and arachnodactyly). The variant arose on two founder haplotypes and results in significantly reduced EMC10 RNA expression and an unstable truncated EMC10 protein. CONCLUSION We propose that a homozygous loss-of-function variant in EMC10 causes a novel syndromic neurodevelopmental phenotype. Remarkably, the recurrent variant is likely the result of a hypermutable site and arose on distinct founder haplotypes.
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Affiliation(s)
- Diane D Shao
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Rachel Straussberg
- Neurogenetics Clinic, Neurology Unit, Schneider Children Medical Center, Petah Tikvah, Israel
- Sackler School of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Hind Ahmed
- Genetics Division, Department of Pediatrics, King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Science, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Amjad Khan
- Genetics Division, Department of Pediatrics, King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Science, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Songhai Tian
- Department of Urology, Boston Children's Hospital, and Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - R Sean Hill
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Richard S Smith
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Amar J Majmundar
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | | | - Jennifer E Neil
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Edward Yang
- Department of Radiology, Boston Children's Hospital, Boston, MA, USA
| | - Amal Al Tenaiji
- Medical Institute of Medical Affairs, Sheikh Khalifa Medica City, Abu Dhabi, UAE
| | - Saumya S Jamuar
- Department of Pediatrics, KK Women's and Children's Hospital, Ramat Aviv, Israel
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
| | - Thorsten M Schlaeger
- Stem Cell Program, Boston Children's Hospital, Harvard Medical School, and Harvard Stem Cell Institute, Harvard University, Boston, MA, USA
| | - Muna Al-Saffar
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, United Arab Emirates University, Abu Dhabi, UAE
| | | | - Aisha Al-Shamsi
- Division of Genetics, Department of Pediatrics, Tawam Hospital, Al Ain, UAE
| | - Lina Basel-Salmon
- Sackler School of Medicine, Tel Aviv University, Ramat Aviv, Israel
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital and Pediatric Genetics Clinic, Schneider Children's Medical Center, and Felsenstein Medical Research Center, Petah Tikvah, Israel
| | - Achiya Z Amir
- Sackler School of Medicine, Tel Aviv University, Ramat Aviv, Israel
- Pediatric Gastroenterology, Hepatology and Nutrition Clinic, Dana-Dwek Children's Hospital, Tel Aviv Medical Center, Ramat Aviv, Israel
| | - Lariza M Rento
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Jiin Ying Lim
- Department of Pediatrics, KK Women's and Children's Hospital, Ramat Aviv, Israel
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Singapore
| | - Indra Ganesan
- Department of Pediatrics, KK Women's and Children's Hospital, Ramat Aviv, Israel
| | - Shirlee Shril
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Gilad Evrony
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- New York University School of Medicine, Center for Human Genetics & Genomics, New York, NY, USA
| | - A James Barkovich
- Neuroradiology, University of California at San Francisco, San Francisco, CA, USA
| | | | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Min Dong
- Department of Urology, Boston Children's Hospital, and Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Guntram Borck
- Center for Rare Diseases (ZSE Ulm), Ulm University Medical Center, Ulm, Germany
- genetikum, Neu-Ulm, Germany
| | | | - Lihadh Al-Gazali
- Department of Pediatrics, United Arab Emirates University, Al Ain, UAE
| | - Wafaa Eyaid
- Genetics Division, Department of Pediatrics, King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Science, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Christopher A Walsh
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.
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