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Liaqat K, Treat K, Mantcheva L, Nasir A, Weaver DD, Conboy E, Vetrini F. A case of MBTPS1-related disorder due to compound heterozygous variants in MBTPS1 gene: Genotype-phenotype expansion and the emergence of a novel syndrome. Am J Med Genet A 2024; 194:e63499. [PMID: 38135440 DOI: 10.1002/ajmg.a.63499] [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: 10/18/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023]
Abstract
MBTPS1 (NM_003791.4) encodes Site-1 protease, a serine protease that functions sequentially with Site-2 protease regulating cholesterol homeostasis and endoplasmic reticulum stress response. MBTPS1 pathogenic variants are associated with spondyloepiphyseal dysplasia, Kondo-Fu type (MIM:618392; cataract, alopecia, oral mucosal disorder, and psoriasis-like syndrome, and Silver-Russell-like syndrome). In this report, we describe a 14-year-old female with a complex medical history including white matter volume loss, early-onset cataracts, retrognathia, laryngomalacia, inguinal hernia, joint hypermobility, feeding dysfunction, and speech delay. Additionally, features of ectodermal dysplasia that she has include decreased sweating, heat intolerance, dysplastic nails, chronically dry skin, and abnormal hair growth issues. Exome sequencing analysis identified compound heterozygous variants in the MBTPS1 gene: c.2255G > T p.(Gly752Val) predicted to affect important function of the protein, which was inherited from the mother, and a splice site variant c.2831 + 5G > T, which was inherited from the father. The RNA-seq analysis of the splice variant showed skipping of exon 21, predicted to result in frameshifting p.(Ser901fs28*) leading to non-sense mediated decay. To our knowledge, only eight studies have been published that described the MBPTS1-related disorders. Interestingly, we observed the features of ectodermal dysplasia in our patient that further expands the phenotypic spectrum of MBTPS1 gene-related disorders.
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Affiliation(s)
- Khurram Liaqat
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Kayla Treat
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Lili Mantcheva
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Abdul Nasir
- Department of Anesthesiology, Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - David D Weaver
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Erin Conboy
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Francesco Vetrini
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
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Bruns R, Liaqat K, Nasir A, Treat K, Murthy VS, Mantcheva L, Torres W, Conboy E, Vetrini F. Undiagnosed rare disease clinic identifies a novel UBE3A variant in two sisters with Angelman syndrome: The end of a diagnostic odyssey. Congenit Anom (Kyoto) 2024. [PMID: 38520260 DOI: 10.1111/cga.12566] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/11/2024] [Accepted: 03/17/2024] [Indexed: 03/25/2024]
Abstract
Angelman syndrome (AS, MIM #105830) is a neurodevelopmental disorder characterized by severe intellectual disability, profound developmental delay, movement or balance problems, an excessively cheerful disposition, and seizures. AS results from inadequate expression of the maternal UBE3A gene (MIM #601623), which encodes an E3 ligase in the ubiquitin-proteasome pathway. Here we present the case of two sisters with features consistent with AS who had negative methylation analyses. An autism/intellectual disability expanded panel revealed a maternally inherited novel UBE3A (NM_001354506.2) variant c.2443C>T p.(Pro815Ser) in both patients that was initially classified as a variant of uncertain significance. The patients were enrolled in Indiana University's Undiagnosed Rare Disease Clinic (URDC) to further investigate the variant. Additional data, including deep phenotyping, familial segregation analysis, and in silico studies, suggest that the variant is likely pathogenic. 3D modeling studies based on the available crystal structure revealed that the Pro815Ser variant can introduce more flexibility into the protein and alter its enzymatic activity. Recent literature confirms the pathogenic nature of the variant. Reanalysis of the UBE3A variant has heightened existing knowledge of AS and has offered this family an end to their diagnostic odyssey.
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Affiliation(s)
- Rebecca Bruns
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Khurram Liaqat
- Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medical and Molecular Genetics, Indiana Univervsity School of Medicine, Indianapolis, Indiana, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Abdul Nasir
- Department of Anesthesiology, Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Kayla Treat
- Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medical and Molecular Genetics, Indiana Univervsity School of Medicine, Indianapolis, Indiana, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Vinaya S Murthy
- Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medical and Molecular Genetics, Indiana Univervsity School of Medicine, Indianapolis, Indiana, USA
| | - Lili Mantcheva
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Wilfredo Torres
- Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medical and Molecular Genetics, Indiana Univervsity School of Medicine, Indianapolis, Indiana, USA
| | - Erin Conboy
- Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medical and Molecular Genetics, Indiana Univervsity School of Medicine, Indianapolis, Indiana, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Francesco Vetrini
- Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medical and Molecular Genetics, Indiana Univervsity School of Medicine, Indianapolis, Indiana, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine, Indianapolis, Indiana, USA
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Buchh M, Gillespie PJ, Treat K, Abreu MA, Schwantes-An THL, Helm BM, Fang F, Xuei X, Mantcheva L, Suhrie KR, Graham BH, Conboy E, Vetrini F. Characterization of a novel deep-intronic variant in DYNC2H1 identified by whole-exome sequencing in a patient with a lethal form of a short-rib thoracic dysplasia type III. Cold Spring Harb Mol Case Stud 2022; 8:a006254. [PMID: 36442996 PMCID: PMC9808550 DOI: 10.1101/mcs.a006254] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/21/2022] [Indexed: 11/30/2022] Open
Abstract
Biallelic pathogenic variants in DYNC2H1 are the cause of short-rib thoracic dysplasia type III with or without polydactyly (OMIM #613091), a skeletal ciliopathy characterized by thoracic hypoplasia due to short ribs. In this report, we review the case of a patient who was admitted to the Neonatal Intensive Care Unit (NICU) of Indiana University Health (IUH) for respiratory support after experiencing respiratory distress secondary to a small, narrow chest causing restrictive lung disease. Additional phenotypic features include postaxial polydactyly, short proximal long bones, and ambiguous genitalia were noted. Exome sequencing (ES) revealed a maternally inherited likely pathogenic variant c.10322C > T p.(Leu3448Pro) in the DYNC2H1 gene. However, there was no variant found on the paternal allele. Microarray analysis to detect deletion or duplication in DYNC2H1 was normal. Therefore, there was insufficient evidence to establish a molecular diagnosis. To further explore the data and perform additional investigations, the patient was subsequently enrolled in the Undiagnosed Rare Disease Clinic (URDC) at Indiana University School of Medicine (IUSM). The investigators at the URDC performed a reanalysis of the ES raw data, which revealed a paternally inherited DYNC2H1 deep-intronic variant c.10606-14A > G predicted to create a strong cryptic acceptor splice site. Additionally, the RNA sequencing of fibroblasts demonstrated partial intron retention predicted to cause a premature stop codon and nonsense-mediated mRNA decay (NMD). Droplet digital RT-PCR (RT-ddPCR) showed a drastic reduction by 74% of DYNCH2H1 mRNA levels. As a result, the intronic variant was subsequently reclassified as likely pathogenic resulting in a definitive clinical and genetic diagnosis for this patient. Reanalysis of ES and fibroblast mRNA experiments confirmed the pathogenicity of the splicing variants to supplement critical information not revealed in original ES or CMA reports. The NICU and URDC collaboration ended the diagnostic odyssey for this family; furthermore, its importance is emphasized by the possibility of prenatally diagnosing the mother's current pregnancy.
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Affiliation(s)
- Muqsit Buchh
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | | | - Kayla Treat
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine. Indianapolis, Indiana 46202, USA
| | - Marco A Abreu
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Tae-Hwi Linus Schwantes-An
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine. Indianapolis, Indiana 46202, USA
| | - Benjamin M Helm
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine. Indianapolis, Indiana 46202, USA
| | - Fang Fang
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Xiaoling Xuei
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Lili Mantcheva
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Kristen R Suhrie
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Brett H Graham
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Erin Conboy
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine. Indianapolis, Indiana 46202, USA
| | - Francesco Vetrini
- Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Undiagnosed Rare Disease Clinic (URDC), Indiana University School of Medicine. Indianapolis, Indiana 46202, USA
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