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Calame DG, Fatih JM, Herman I, Coban‐Akdemir Z, Du H, Mitani T, Jhangiani SN, Marafi D, Gibbs RA, Posey JE, Mehta VP, Mohila CA, Abid F, Lotze TE, Pehlivan D, Adesina AM, Lupski JR. Deep clinicopathological phenotyping identifies a previously unrecognized pathogenic EMD splice variant. Ann Clin Transl Neurol 2021; 8:2052-2058. [PMID: 34524739 PMCID: PMC8528454 DOI: 10.1002/acn3.51454] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/12/2021] [Accepted: 09/02/2021] [Indexed: 12/05/2022] Open
Abstract
Exome sequencing (ES) has revolutionized rare disease management, yet only ~25%-30% of patients receive a molecular diagnosis. A limiting factor is the quality of available phenotypic data. Here, we describe how deep clinicopathological phenotyping yielded a molecular diagnosis for a 19-year-old proband with muscular dystrophy and negative clinical ES. Deep phenotypic analysis identified two critical data points: (1) the absence of emerin protein in muscle biopsy and (2) clinical features consistent with Emery-Dreifuss muscular dystrophy. Sequencing data analysis uncovered an ultra-rare, intronic variant in EMD, the gene encoding emerin. The variant, NM_000117.3: c.188-6A > G, is predicted to impact splicing by in silico tools. This case thus illustrates how better integration of clinicopathologic data into ES analysis can enhance diagnostic yield with implications for clinical practice.
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Affiliation(s)
- Daniel G. Calame
- Division of Neurology and Developmental NeuroscienceDepartment of PediatricsBaylor College of MedicineHoustonTexas77030USA
- Texas Children’s HospitalHoustonTexas77030USA
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas77030USA
| | - Jawid M. Fatih
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas77030USA
| | - Isabella Herman
- Division of Neurology and Developmental NeuroscienceDepartment of PediatricsBaylor College of MedicineHoustonTexas77030USA
- Texas Children’s HospitalHoustonTexas77030USA
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas77030USA
| | - Zeynep Coban‐Akdemir
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas77030USA
| | - Haowei Du
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas77030USA
| | - Tadahiro Mitani
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas77030USA
| | | | - Dana Marafi
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas77030USA
- Department of PediatricsFaculty of MedicineKuwait UniversitySafat13110Kuwait
| | - Richard A. Gibbs
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas77030USA
- Human Genome Sequencing CenterBaylor College of MedicineHoustonTexas77030USA
| | - Jennifer E. Posey
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas77030USA
| | - Vidya P. Mehta
- Department of PathologyTexas Children's HospitalBaylor College of MedicineHoustonTexas77030USA
| | - Carrie A. Mohila
- Department of PathologyTexas Children's HospitalBaylor College of MedicineHoustonTexas77030USA
| | - Farida Abid
- Division of Neurology and Developmental NeuroscienceDepartment of PediatricsBaylor College of MedicineHoustonTexas77030USA
- Texas Children’s HospitalHoustonTexas77030USA
| | - Timothy E. Lotze
- Division of Neurology and Developmental NeuroscienceDepartment of PediatricsBaylor College of MedicineHoustonTexas77030USA
- Texas Children’s HospitalHoustonTexas77030USA
| | - Davut Pehlivan
- Division of Neurology and Developmental NeuroscienceDepartment of PediatricsBaylor College of MedicineHoustonTexas77030USA
- Texas Children’s HospitalHoustonTexas77030USA
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas77030USA
| | - Adekunle M. Adesina
- Department of PathologyTexas Children's HospitalBaylor College of MedicineHoustonTexas77030USA
| | - James R. Lupski
- Texas Children’s HospitalHoustonTexas77030USA
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas77030USA
- Human Genome Sequencing CenterBaylor College of MedicineHoustonTexas77030USA
- Department of PediatricsBaylor College of MedicineHoustonTexas77030USA
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Saad AK, Marafi D, Mitani T, Jolly A, Du H, Elbendary HM, Jhangiani SN, Akdemir ZC, Gibbs RA, Hunter JV, Carvalho CMBC, Pehlivan D, Posey JE, Zaki MS, Lupski JR. Biallelic in-frame deletion in TRAPPC4 in a family with developmental delay and cerebellar atrophy. Brain 2020; 143:e83. [PMID: 33011761 PMCID: PMC7586085 DOI: 10.1093/brain/awaa256] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Ahmed K Saad
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Medical Molecular Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, P.O. Box 24923, 13110 Safat, Kuwait
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- MD/PhD Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Hasnaa M Elbendary
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | | | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jill V Hunter
- Department of Radiology, Baylor College of Medicine, Houston, Texas, 77030, USA
- E.B. Singleton Department of Pediatric Radiology, Texas Children's Hospital, Houston, Texas, 77030, USA
| | - Claudia M B C Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Maha S Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
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