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Lo E, Blair J, Yamamoto N, Diaz-Miranda MA, Bedoukian E, Gray C, Lawrence A, Dedhia K, Elden LM, Germiller JA, Kazahaya K, Sobol SE, Luo M, Krantz ID, Hartman TR. Recurrent missense variant identified in two unrelated families with MPZL2-related hearing loss, expanding the variant spectrum associated with DFNB111. Am J Med Genet A 2024; 194:e63530. [PMID: 38197511 DOI: 10.1002/ajmg.a.63530] [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] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/17/2023] [Accepted: 12/22/2023] [Indexed: 01/11/2024]
Abstract
MPZL2-related hearing loss is a rare form of autosomal recessive hearing loss characterized by progressive, mild sloping to severe sensorineural hearing loss. Thirty-five previously reported patients had biallelic truncating variants in MPZL2, with the exception of one patient with a missense variant of uncertain significance and a truncating variant. Here, we describe the clinical characteristics and genotypes of five patients from four families with confirmed MPZL2-related hearing loss. A rare missense likely pathogenic variant [NM_005797.4(MPZL2):c.280C>T,p.(Arg94Trp)] located in exon 3 was confirmed to be in trans with a recurrent pathogenic truncating variant that segregated with hearing loss in three of the patients from two unrelated families. This is the first recurrent likely pathogenic missense variant identified in MPZL2. Apparently milder or later-onset hearing loss associated with rare missense variants in MPZL2 indicates that some missense variants in this gene may cause a milder phenotype than that resulting from homozygous or compound heterozygous truncating variants. This study, along with the identification of truncating loss of function and missense MPZL2 variants in several diverse populations, suggests that MPZL2-related hearing loss may be more common than previously appreciated and demonstrates the need for MPZL2 inclusion in hearing loss testing panels.
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Affiliation(s)
- Emma Lo
- Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Justin Blair
- Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nobuko Yamamoto
- Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Otolaryngology, Department of Surgical Specialties, National Center for Children's Health and Development, Tokyo, Japan
| | - Maria Alejandra Diaz-Miranda
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Emma Bedoukian
- Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Christopher Gray
- Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Audrey Lawrence
- Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kavita Dedhia
- Division of Otolaryngology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Otorhinolaryngology - Head and Neck Surgery, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lisa M Elden
- Division of Otolaryngology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Otorhinolaryngology - Head and Neck Surgery, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John A Germiller
- Division of Otolaryngology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Otorhinolaryngology - Head and Neck Surgery, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ken Kazahaya
- Division of Otolaryngology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Otorhinolaryngology - Head and Neck Surgery, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Steven E Sobol
- Division of Otolaryngology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Otorhinolaryngology - Head and Neck Surgery, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Minjie Luo
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ian D Krantz
- Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Tiffiney R Hartman
- Roberts Individualized Medical Genetics Center (RIMGC), Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Translational Medicine and Human Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Pan Z, Theesfeld CL. Deciphering missense coding variants with AlphaMissense. Kidney Int 2024:S0085-2538(24)00190-X. [PMID: 38647510 DOI: 10.1016/j.kint.2024.02.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/12/2024] [Indexed: 04/25/2024]
Affiliation(s)
- Zhicheng Pan
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, New York, USA
| | - Chandra L Theesfeld
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA.
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Oto Y, Suzuki D, Morita T, Inoue T, Nitta A, Murakami N, Abe Y, Hamada Y, Akiyama T, Matsubara T. A case report of odonto-hypophosphatasia with a novel variant in the ALPL gene. J Pediatr Endocrinol Metab 2024; 37:276-279. [PMID: 38310522 DOI: 10.1515/jpem-2023-0549] [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: 12/13/2023] [Accepted: 01/16/2024] [Indexed: 02/06/2024]
Abstract
OBJECTIVES Hypophosphatasia (HPP) is a rare skeletal dysplasia caused by variants in the alkaline phosphatase (ALPL) gene. More than 400 pathogenic variants of the ALPL gene have been registered in the ALPL gene variant database. Here, we describe the case of a Japanese child with odonto-hypophsphatasia (odonto-HPP) and a novel ALPL variant. CASE PRESENTATION At the age of 2 years and 1 month, he prematurely lost one deciduous tooth, with the root intact, when he fell and hit his face lightly. Three months later, he lost another adjacent deciduous tooth without incentive. His serum alkaline phosphatase (ALP) level was 72 U/L. His urine phosphoethanolamine (PEA) level was extremely high at 938 μmol/mg·Cre. The serum pyridoxal 5'-phosphaye (PLP) level was 255.9 nmol/L. Based on the clinical symptoms and laboratory findings, the patient was clinically diagnosed with odonto-HPP. Genetic analysis of the ALPL gene revealed a heterozygous variant (NM_000478.6:c.1151C>A, p.Thr384Lys). CONCLUSIONS We report a case of odonto-HPP with a novel variant in the ALPL gene. HPP is a rare disease, and the heterozygous mutation in the ALPL gene highlights the novelty of this case.
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Affiliation(s)
- Yuji Oto
- Department of Pediatrics, Dokkyo Medical University Saitama Medical Center, Saitama, Japan
| | - Daiki Suzuki
- Department of Pediatrics, Dokkyo Medical University Saitama Medical Center, Saitama, Japan
| | - Tsubasa Morita
- Department of Pediatrics, Dokkyo Medical University Saitama Medical Center, Saitama, Japan
| | - Takeshi Inoue
- Child Development and Psychosomatic Medicine Center, Dokkyo Medical University Saitama Medical Center, Saitama, Japan
| | - Akihisa Nitta
- Department of Pediatrics, Dokkyo Medical University Saitama Medical Center, Saitama, Japan
| | - Nobuyuki Murakami
- Department of Pediatrics, Dokkyo Medical University Saitama Medical Center, Saitama, Japan
| | - Yuuka Abe
- Center for Genetic Medicine, Dokkyo Medical University Saitama Medical Center, Saitama, Japan
| | - Yoshinobu Hamada
- Center for Genetic Medicine, Dokkyo Medical University Saitama Medical Center, Saitama, Japan
| | - Tomoyuki Akiyama
- Department of Pediatrics (Child Neurology), Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Tomoyo Matsubara
- Department of Pediatrics, Dokkyo Medical University Saitama Medical Center, Saitama, Japan
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Weston TGR, Rees M, Gautel M, Fraternali F. Walking with giants: The challenges of variant impact assessment in the giant sarcomeric protein titin. WIREs Mech Dis 2024; 16:e1638. [PMID: 38155593 DOI: 10.1002/wsbm.1638] [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: 06/15/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/30/2023]
Abstract
Titin, the so-called "third filament" of the sarcomere, represents a difficult challenge for the determination of damaging genetic variants. A single titin molecule extends across half the length of a sarcomere in striated muscle, fulfilling a variety of vital structural and signaling roles, and has been linked to an equally varied range of myopathies, resulting in a significant burden on individuals and healthcare systems alike. While the consequences of truncating variants of titin are well-documented, the ramifications of the missense variants prevalent in the general population are less so. We here present a compendium of titin missense variants-those that result in a single amino-acid substitution in coding regions-reported to be pathogenic and discuss these in light of the nature of titin and the variant position within the sarcomere and their domain, the structural, pathological, and biophysical characteristics that define them, and the methods used for characterization. Finally, we discuss the current knowledge and integration of the multiple fields that have contributed to our understanding of titin-related pathology and offer suggestions as to how these concurrent methodologies may aid the further development in our understanding of titin and hopefully extend to other, less well-studied giant proteins. This article is categorized under: Cardiovascular Diseases > Genetics/Genomics/Epigenetics Congenital Diseases > Genetics/Genomics/Epigenetics Congenital Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Timir G R Weston
- Randall Centre for Cell & Molecular Biophysics, King's College London, London, UK
| | - Martin Rees
- Randall Centre for Cell & Molecular Biophysics, King's College London, London, UK
| | - Mathias Gautel
- Randall Centre for Cell & Molecular Biophysics, King's College London, London, UK
| | - Franca Fraternali
- Institute of Structural and Molecular Biology, University College London, London, UK
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Zhao H, Du H, Zhao S, Chen Z, Li Y, Xu K, Liu B, Cheng X, Wen W, Li G, Chen G, Zhao Z, Qiu G, Liu P, Zhang TJ, Wu Z, Wu N. SIGMA leverages protein structural information to predict the pathogenicity of missense variants. Cell Rep Methods 2024; 4:100687. [PMID: 38211594 PMCID: PMC10831939 DOI: 10.1016/j.crmeth.2023.100687] [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] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/15/2023] [Accepted: 12/14/2023] [Indexed: 01/13/2024]
Abstract
Leveraging protein structural information to evaluate pathogenicity has been hindered by the scarcity of experimentally determined 3D protein. With the aid of AlphaFold2 predictions, we developed the structure-informed genetic missense mutation assessor (SIGMA) to predict missense variant pathogenicity. In comparison with existing predictors across labeled variant datasets and experimental datasets, SIGMA demonstrates superior performance in predicting missense variant pathogenicity (AUC = 0.933). We found that the relative solvent accessibility of the mutated residue contributed greatly to the predictive ability of SIGMA. We further explored combining SIGMA with other top-tier predictors to create SIGMA+, proving highly effective for variant pathogenicity prediction (AUC = 0.966). To facilitate the application of SIGMA, we pre-computed SIGMA scores for over 48 million possible missense variants across 3,454 disease-associated genes and developed an interactive online platform (https://www.sigma-pred.org/). Overall, by leveraging protein structure information, SIGMA offers an accurate structure-based approach to evaluating the pathogenicity of missense variants.
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Affiliation(s)
- Hengqiang Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Huakang Du
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Zefu Chen
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Yaqi Li
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Kexin Xu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Bowen Liu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Xi Cheng
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Wen Wen
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Guozhuang Li
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Guilin Chen
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Zhengye Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China.
| | - Zhihong Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China; Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing 100730, China.
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China.
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Tian W, Li H, Li Y, Guo J, Wang H, Yang B, Li P, Cui X, Liu L. A novel missense variant in OTUD5 causes X-linked multiple congenital anomalies-neurodevelopmental syndrome. Mol Genet Genomic Med 2024; 12:e2325. [PMID: 38037881 PMCID: PMC10767676 DOI: 10.1002/mgg3.2325] [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: 07/13/2023] [Revised: 10/13/2023] [Accepted: 11/10/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND The OTUD5 gene encodes a deubiquitinating enzyme (DUB) of the OTU family. Variants of OTUD5 are associated with X-linked multiple congenital anomalies-neurodevelopmental syndrome (MCAND). The case described in this study expands the clinical and molecular spectrum of OTUD5. METHODS Trio-based clinical exome sequencing (trio-CES) was performed on a Chinese boy with a clinical phenotype and both of his parents. Sanger sequencing was employed for validation of the variant detected. RESULTS The patient presented with characteristic facial features, intellectual disability, motor/language/cognitive, and global developmental delays, limb contractures, and kidney abnormalities, and trio-CES identified a de novo missense variant, c.1305T>A, of the OTUD5 gene. DISCUSSION We describe OTUD5 gene variation in the Chinese population, with the first report of this variant. Additionally, we provide a comprehensive summary of all published cases of MCAND to date, in order to elucidate the primary clinical features of the syndrome and the variability in phenotype severity. This case expands the genetic and clinical phenotypic spectrum of OTUD5-associated MCAND.
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Affiliation(s)
- Weifang Tian
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Haiyu Li
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Ying Li
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Jing Guo
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Handuo Wang
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Bo Yang
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Pengyun Li
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Xueyin Cui
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
| | - Ling Liu
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan ProvinceZhengzhouChina
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Jain K, McCarley SC, Mukhtar G, Ferlin A, Fleming A, Morris-Rosendahl DJ, Shovlin CL. Pathogenic Variant Frequencies in Hereditary Haemorrhagic Telangiectasia Support Clinical Evidence of Protection from Myocardial Infarction. J Clin Med 2023; 13:250. [PMID: 38202257 PMCID: PMC10779873 DOI: 10.3390/jcm13010250] [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] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Hereditary haemorrhagic telangiectasia (HHT) is a vascular dysplasia inherited as an autosomal dominant trait, due to a single heterozygous loss-of-function variant, usually in ACVRL1 (encoding activin receptor-like kinase 1 [ALK1]), ENG (encoding endoglin [CD105]), or SMAD4. In a consecutive single-centre series of 37 positive clinical genetic tests performed in 2021-2023, a skewed distribution pattern was noted, with 30 of 32 variants reported only once, but ACVRL1 c.1231C>T (p.Arg411Trp) identified as the disease-causal gene in five different HHT families. In the same centre's non-overlapping 1992-2020 series where 110/134 (82.1%) HHT-causal variants were reported only once, ACVRL1 c.1231C>T (p.Arg411Trp) was identified in nine further families. In a 14-country, four-continent HHT Mutation Database where 181/250 (72.4%) HHT-causal variants were reported only once, ACVRL1 c.1231C>T (p.Arg411Trp) was reported by 12 different laboratories, the adjacent ACVRL1 c.1232G>A (p.Arg411Gln) by 14, and ACVRL1 c.1120C>T (p.Arg374Trp) by 18. Unlike the majority of HHT-causal ACVRL1 variants, these encode ALK1 protein that reaches the endothelial cell surface but fails to signal. Six variants of this type were present in the three series and were reported 6.8-25.5 (mean 8.9) times more frequently than the other ACVRL1 missense variants (all p-values < 0.0039). Noting lower rates of myocardial infarction reported in HHT, we explore potential mechanisms, including a selective paradigm relevant to ALK1's role in the initiating event of atherosclerosis, where a plausible dominant negative effect of these specific variants can be proposed. In conclusion, there is an ~9-fold excess of kinase-inactive, cell surface-expressed ACVRL1/ALK1 pathogenic missense variants in HHT. The findings support further examination of differential clinical and cellular phenotypes by HHT causal gene molecular subtypes.
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Affiliation(s)
- Kinshuk Jain
- National Heart and Lung Institute, Imperial College London, London W12 0NN, UK; (K.J.); (S.C.M.); (G.M.); (D.J.M.-R.)
| | - Sarah C. McCarley
- National Heart and Lung Institute, Imperial College London, London W12 0NN, UK; (K.J.); (S.C.M.); (G.M.); (D.J.M.-R.)
| | - Ghazel Mukhtar
- National Heart and Lung Institute, Imperial College London, London W12 0NN, UK; (K.J.); (S.C.M.); (G.M.); (D.J.M.-R.)
| | - Anna Ferlin
- Clinical Genetics and Genomics Laboratory, Royal Brompton Hospital, Guy’s and St Thomas’ NHS Trust, London SE1 7EH, UK; (A.F.); (A.F.)
| | - Andrew Fleming
- Clinical Genetics and Genomics Laboratory, Royal Brompton Hospital, Guy’s and St Thomas’ NHS Trust, London SE1 7EH, UK; (A.F.); (A.F.)
| | - Deborah J. Morris-Rosendahl
- National Heart and Lung Institute, Imperial College London, London W12 0NN, UK; (K.J.); (S.C.M.); (G.M.); (D.J.M.-R.)
- Clinical Genetics and Genomics Laboratory, Royal Brompton Hospital, Guy’s and St Thomas’ NHS Trust, London SE1 7EH, UK; (A.F.); (A.F.)
| | - Claire L. Shovlin
- National Heart and Lung Institute, Imperial College London, London W12 0NN, UK; (K.J.); (S.C.M.); (G.M.); (D.J.M.-R.)
- Specialist Medicine, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London W12 0HS, UK
- Social, Genetic and Environmental Determinants of Health, NIHR Imperial Biomedical Research Centre, London W2 1NY, UK
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8
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McCarley SC, Murphy DA, Thompson J, Shovlin CL. Pharmacogenomic Considerations for Anticoagulant Prescription in Patients with Hereditary Haemorrhagic Telangiectasia. J Clin Med 2023; 12:7710. [PMID: 38137783 PMCID: PMC10744266 DOI: 10.3390/jcm12247710] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Hereditary haemorrhagic telangiectasia (HHT) is a vascular dysplasia that commonly results in bleeding but with frequent indications for therapeutic anticoagulation. Our aims were to advance the understanding of drug-specific intolerance and evaluate if there was an indication for pharmacogenomic testing. Genes encoding proteins involved in the absorption, distribution, metabolism, and excretion of warfarin, heparin, and direct oral anticoagulants (DOACs) apixaban, rivaroxaban, edoxaban, and dabigatran were identified and examined. Linkage disequilibrium with HHT genes was excluded, before variants within these genes were examined following whole genome sequencing of general and HHT populations. The 44 genes identified included 5/17 actionable pharmacogenes with guidelines. The 76,156 participants in the Genome Aggregation Database v3.1.2 had 28,446 variants, including 9668 missense substitutions and 1076 predicted loss-of-function (frameshift, nonsense, and consensus splice site) variants, i.e., approximately 1 in 7.9 individuals had a missense substitution, and 1 in 71 had a loss-of-function variant. Focusing on the 17 genes relevant to usually preferred DOACs, similar variant profiles were identified in HHT patients. With HHT patients at particular risk of haemorrhage when undergoing anticoagulant treatment, we explore how pre-emptive pharmacogenomic testing, alongside HHT gene testing, may prove beneficial in reducing the risk of bleeding and conclude that HHT patients are well placed to be at the vanguard of personalised prescribing.
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Affiliation(s)
- Sarah C. McCarley
- National Heart and Lung Institute, Imperial College London, London W12 0NN, UK; (S.C.M.); (J.T.)
| | - Daniel A. Murphy
- Pharmacy Department, Imperial College Healthcare NHS Trust, London W2 1NY, UK;
- Social, Genetic and Envionmental Determinants of Health Theme, NIHR Imperial Biomedical Research Centre, London W2 1NY, UK
| | - Jack Thompson
- National Heart and Lung Institute, Imperial College London, London W12 0NN, UK; (S.C.M.); (J.T.)
| | - Claire L. Shovlin
- National Heart and Lung Institute, Imperial College London, London W12 0NN, UK; (S.C.M.); (J.T.)
- Social, Genetic and Envionmental Determinants of Health Theme, NIHR Imperial Biomedical Research Centre, London W2 1NY, UK
- Specialist Medicine, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London W12 0HS, UK
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Mitok KA, Schueler KL, King SM, Orr J, Ryan KA, Keller MP, Krauss RM, Mitchell BD, Shuldiner AR, Attie AD. Missense variants in SORT1 are associated with LDL-C in an Amish population. J Lipid Res 2023; 64:100468. [PMID: 37913995 PMCID: PMC10711479 DOI: 10.1016/j.jlr.2023.100468] [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: 08/09/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/03/2023] Open
Abstract
Common noncoding variants at the human 1p13.3 locus associated with SORT1 expression are among those most strongly associated with low-density lipoprotein cholesterol (LDL-C) in human genome-wide association studies. However, validation studies in mice and cell lines have produced variable results regarding the directionality of the effect of SORT1 on LDL-C. This, together with the fact that the 1p13.3 variants are associated with expression of several genes, has raised the question of whether SORT1 is the causal gene at this locus. Using whole exome sequencing in members of an Amish population, we identified coding variants in SORT1 that are associated with increased (rs141749679, K302E) and decreased (rs149456022, Q225H) LDL-C. Further, analysis of plasma lipoprotein particle subclasses by ion mobility in a subset of rs141749679 (K302E) carriers revealed higher levels of large LDL particles compared to noncarriers. In contrast to the effect of these variants in the Amish, the sortilin K302E mutation introduced into a C57BL/6J mouse via CRISPR/Cas9 resulted in decreased non-high-density lipoprotein cholesterol, and the sortilin Q225H mutation did not alter cholesterol levels in mice. This is indicative of different effects of these mutations on cholesterol metabolism in the two species. To our knowledge, this is the first evidence that naturally occurring coding variants in SORT1 are associated with LDL-C, thus supporting SORT1 as the gene responsible for the association of the 1p13.3 locus with LDL-C.
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Affiliation(s)
- Kelly A Mitok
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Kathryn L Schueler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Sarah M King
- Department of Pediatrics, University of California-San Francisco, San Francisco, CA, USA
| | - Joseph Orr
- Department of Pediatrics, University of California-San Francisco, San Francisco, CA, USA
| | - Kathleen A Ryan
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mark P Keller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ronald M Krauss
- Department of Pediatrics, University of California-San Francisco, San Francisco, CA, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alan R Shuldiner
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA; Regeneron Genetics Center, Tarrytown, NY, USA
| | - Alan D Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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Li J, Zhang F, Xu M, Qiu H, Zhou C, Li L, Qin L. Case Report: A combination of chimeric CYP11B2/CYP11B1 and a novel p.Val68Gly CYP11B1 variant causing 11β-Hydroxylase deficiency in a Chinese patient. Front Endocrinol (Lausanne) 2023; 14:1216767. [PMID: 38027139 PMCID: PMC10679387 DOI: 10.3389/fendo.2023.1216767] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction 11β-Hydroxylase deficiency (11β-OHD, OMIM#202010) is the second most common form of congenital adrenal hyperplasia (CAH) caused by pathogenic variants in the CYP11B1 gene. Both single nucleotide variations (SNV)/small insertion and deletion and genomic rearrangements of CYP11B1 are important causes of 11β-OHD. Among these variant types, pathogenic CYP11B2/CYP11B1 chimeras only contribute to a minority of cases. Heterozygote cases (chimera combined with SNV) are very rare, and genetic analysis of these cases can be challenging. Case presentation We presented a suspected 11β-OHD female patient with incomplete virilization, adrenal hyperplasia, and hypokalemia hypertension. Whole exome sequencing (WES) revealed that the patient carried both a chimeric CYP11B2/CYP11B1 and a novel missense variant, NM_000497.4: c.203T>G, p.Val68Gly (chr8:143961027) in CYP11B1, which were confirmed by CNVplex and Sanger sequencing, respectively. The patient's manifestations and genetic findings confirmed the diagnosis of 11β-OHD, and oral dexamethasone was administered as a subsequent treatment. Conclusion This report showed a rare CYP11B2/CYP11B1 chimera combined with a novel missense variant in a 11β-OHD female patient. The result expands variant spectrum of CYP11B1 and suggests that both chimera and CYP11B1 variant screening should be performed simultaneously in suspected cases of 11β-OHD. To our knowledge, this is the first report about CYP11B2/CYP11B1 chimera detected by WES analysis. WES combined with CNV analysis is an efficient method in the genetic diagnosis of this rare and complex disorder.
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Affiliation(s)
- Jialin Li
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Fenglan Zhang
- Clincal Genomics Center, Dian Diagnostics Group Co., Ltd., Hangzhou, China
| | - Miao Xu
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Hao Qiu
- Clincal Genomics Center, Dian Diagnostics Group Co., Ltd., Hangzhou, China
| | - Cheng Zhou
- Department of Urology, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Li Li
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Lan Qin
- Clincal Genomics Center, Dian Diagnostics Group Co., Ltd., Hangzhou, China
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Xu H, Wang C, Wei H, Li T, Fang Y, Wang B. A novel missense variant in LAMC1 identified in a POI family by whole exome sequencing. Gynecol Endocrinol 2023; 39:2265507. [PMID: 37839437 DOI: 10.1080/09513590.2023.2265507] [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: 05/01/2023] [Accepted: 09/26/2023] [Indexed: 10/17/2023] Open
Abstract
OBJECTIVE This study aimed to identify novel pathogenic genes and variants in a Chinese family with premature ovarian insufficiency (POI). METHODS A Chinese POI family was enrolled in this study. Whole exome sequencing was performed on the proband and her mother to identify the potential causative genes and variants and Sanger sequencing was used to confirm the finally identified potential pathogenic variant in the family. RESULTS An assessment of the family pedigree suggested that POI was inherited in an autosomal dominant manner in this family. A novel missense variant of the laminin subunit gamma-1 gene (LAMC1; NM_002293.4: c.3281A > T, p.D1094V) was finally identified in the proband and her affected mother. This variant was not found in any public databases. In silico analysis indicated the amino acid encoded at the variant site was highly conserved among mammals and associated with decreased protein stability and disrupted protein function. Its presence in the POI family was confirmed by Sanger sequencing. CONCLUSIONS This study firstly reported a novel missense variant of LAMC1 in a Chinese POI family, which was inherited in an autosomal dominant manner. This variant may result in the development of POI. Our results provide supporting evidence for a causative role for LAMC1 variants in POI.
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Affiliation(s)
- Huanfang Xu
- Institute of Acupuncture and Moxibustion, China Academy of Chinese Medical Sciences, Beijing, China
- Acupuncture and Moxibustion Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Chunyan Wang
- Graduate School of Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
- Center for Genetics, National Research Institute for Family Planning, Beijing, China
| | - Han Wei
- Graduate School of Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
- Center for Genetics, National Research Institute for Family Planning, Beijing, China
| | - Tengyan Li
- Center for Genetics, National Research Institute for Family Planning, Beijing, China
| | - Yigong Fang
- Institute of Acupuncture and Moxibustion, China Academy of Chinese Medical Sciences, Beijing, China
- Acupuncture and Moxibustion Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Binbin Wang
- Graduate School of Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
- Center for Genetics, National Research Institute for Family Planning, Beijing, China
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Dias A, Santos M, Carvalho E, Felício D, Silva P, Alves I, Pinho T, Sousa A, Alves-Ferreira M, Lemos C. Functional characterization of a novel PRRT2 variant found in a Portuguese patient with hemiplegic migraine. Clin Genet 2023; 104:479-485. [PMID: 37243399 DOI: 10.1111/cge.14379] [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] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/08/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023]
Abstract
Familial hemiplegic migraine (FHM) is a rare autosomal-dominant form of migraine with aura. Three disease-causing genes have been identified for FHM: CACNA1A, ATP1A2 and SCN1A. However, not all families are linked to one of these three genes.PRRT2 variants were also commonly associated with HM symptoms; therefore, PRRT2 is hypothesized as the fourth gene causing FHM. PRRT2 plays an important role in neuronal migration, spinogenesis, and synapse mechanisms during development and calcium-dependent neurotransmitter release. We performed exome sequencing to unravel the genetic cause of migraine in one family, and a novel PRRT2 variant (c.938C > T;p.Ala313Val) was identified with further functional studies to confirm its pathogenicity. PRRT2-A313V reduced protein stability, led to protein premature degradation by the proteasome and altered the subcellular localization of PRRT2 from the plasma membrane (PM) to the cytoplasm. We identified and characterized for the first time in a Portuguese patient, a novel heterozygous missense variant in PRRT2 associated with HM symptoms. We suggest that PRRT2 should be included in the diagnosis of HM.
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Affiliation(s)
- Andreia Dias
- UnIGENe, IBMC - Instituto de Biologia Celular e Molecular, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- ICBAS, Instituto Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Mariana Santos
- UnIGENe, IBMC - Instituto de Biologia Celular e Molecular, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Estefânia Carvalho
- UnIGENe, IBMC - Instituto de Biologia Celular e Molecular, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- ICBAS, Instituto Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Daniela Felício
- UnIGENe, IBMC - Instituto de Biologia Celular e Molecular, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- ICBAS, Instituto Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Paulo Silva
- UnIGENe, IBMC - Instituto de Biologia Celular e Molecular, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- CGPP, Centro de Genética Preditiva e Preventiva, IBMC - Instituto de Biologia Celular e Molecular, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Ivânia Alves
- Serviço de Neurologia, Centro Hospitalar Tâmega e Sousa, Penafiel, Portugal
| | - Teresa Pinho
- UnIGENe, IBMC - Instituto de Biologia Celular e Molecular, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- UNIPRO-Oral Pathology and Rehabilitation Research Unit, University Institute of Health Sciences (IUCS), CESPU, Gandra, Portugal
| | - Alda Sousa
- UnIGENe, IBMC - Instituto de Biologia Celular e Molecular, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- ICBAS, Instituto Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Miguel Alves-Ferreira
- UnIGENe, IBMC - Instituto de Biologia Celular e Molecular, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- ICBAS, Instituto Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
- CGPP, Centro de Genética Preditiva e Preventiva, IBMC - Instituto de Biologia Celular e Molecular, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Carolina Lemos
- UnIGENe, IBMC - Instituto de Biologia Celular e Molecular, i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- ICBAS, Instituto Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
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Jesus-Ribeiro J, Pires LM, Ribeiro IP, Rebelo O, Pereira R, Sales F, Santana I, Freire A, Melo JB. The Challenge of Somatic Variants in Focal Cortical Dysplasia. Innov Clin Neurosci 2023; 20:35-39. [PMID: 38193103 PMCID: PMC10773600] [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] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Objective The advent of next-generation sequencing (NGS) enabled the detection of low-level brain somatic variants in postsurgical tissue of focal cortical dysplasia (FCD). The genetic background of FCD Type I remains elusive, while the mammalian target of rapamycin (mTOR) pathway seems to have a relevant role in the pathogenesis of FCD Type II. Our goal was to uncover information on the molecular basis of FCD, performing whole genome sequencing (WGS) in postsurgical tissue to detect candidate brain-specific somatic variants, and evaluate their clinical significance. Design WGS was performed using paired peripheral venous blood and postsurgical pathological brain deoxyribonucleic acid (DNA) samples. Libraries were prepared using the Roche KAPA HyperPrep polymerase chain reaction (PCR) free library preparation kit. Paired-end 150bp reads were generated on the Illumina NovaSeq platform. The FASTQ files were processed using the nf-core sarek pipeline (version 3.0) to call somatic variants, which were then annotated with ANNOVAR. A screening strategy was applied to obtain relevant variants. Results Two female patients with drug-resistant epilepsy due to FCD who underwent surgical treatment were included. Regarding neuropathological diagnosis, one patient had FCD Type Ia and the other had FCD Type IIa. Five somatic nonsynonymous single nucleotide variants (SNVs) were detected using WGS, three in FCD Ia tissue (WDR24 p.Trp259Gly; MICAL1 p.Lys1036Arg; and KATNB1 p.Leu566Ile) and two in FCD IIa tissue (MATN4 p.Phe91Val and ANKRD6 p.His386Gln). All variants were predicted to be potentially pathogenic by at least two different tools. However, they were classified as variants of uncertain significance (VUS) according to the American College of Medical Genetics and Genomics (ACMG) criteria. Conclusion Brain-specific somatic missense variants were identified by NGS in new candidate genes (WDR24, MICAL1, KATNB1, MATN4, and ANKRD6) using postsurgical FCD tissue, which may contribute to further understanding of the genetic background of FCD. All the reported genes were previously related to epilepsy and/or malformations of central nervous system (CNS) and cortical development. However, the pathogenicity assessment of these variants and, consequently, their impact on clinical practice still poses an important challenge.
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Affiliation(s)
- Joana Jesus-Ribeiro
- Dr. Jesus-Ribeiro is with Neurology Department, Centro Hospitalar de Leiria in Leiria, Portugal
- Drs. Jesus-Ribeiro, Ribeiro, and Melo and Mr. Pires are with Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment, Genetics, and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra in Coimbra, Portugal
| | - Luís Miguel Pires
- Drs. Jesus-Ribeiro, Ribeiro, and Melo and Mr. Pires are with Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment, Genetics, and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra in Coimbra, Portugal
- Drs. Ribeiro and Melo and Mr. Pires are also with Laboratory of Cytogenetics and Genomics, Faculty of Medicine, University of Coimbra in Coimbra, Portugal
| | - Ilda Patrícia Ribeiro
- Drs. Jesus-Ribeiro, Ribeiro, and Melo and Mr. Pires are with Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment, Genetics, and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra in Coimbra, Portugal
- Drs. Ribeiro and Melo and Mr. Pires are also with Laboratory of Cytogenetics and Genomics, Faculty of Medicine, University of Coimbra in Coimbra, Portugal
| | - Olinda Rebelo
- Dr. Rebelo is with Neuropathology Laboratory, Neurology Department, Centro Hospitalar e Universitário de Coimbra in Coimbra, Portugal
| | - Ricardo Pereira
- Dr. Pereira is with Neurosurgery Department, Centro Hospitalar e Universitário de Coimbra in Coimbra, Portugal
| | - Francisco Sales
- Dr. Sales is with Epilepsy and Sleep Monitoring Unit, Neurology Department, Centro Hospitalar e Universitário de Coimbra in Coimbra, Portugal
| | - Isabel Santana
- Dr. Santana is with Neurology Department, Centro Hospitalar e Universitário de Coimbra in Coimbra, Portugal
- Drs. Santana and Freire are with Faculty of Medicine, University of Coimbra in Coimbra, Portugal
| | - António Freire
- Drs. Santana and Freire are with Faculty of Medicine, University of Coimbra in Coimbra, Portugal
- Dr. Freire is also with Neurology Department, Luz Hospital in Coimbra, Portugal
| | - Joana Barbosa Melo
- Drs. Jesus-Ribeiro, Ribeiro, and Melo and Mr. Pires are with Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment, Genetics, and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra in Coimbra, Portugal
- Drs. Ribeiro and Melo and Mr. Pires are also with Laboratory of Cytogenetics and Genomics, Faculty of Medicine, University of Coimbra in Coimbra, Portugal
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Lee DJ, Kim Y, Dinh PTN, Chung Y, Lee D, Kim Y, Lee SH, Choi I, Lee SH. Identification of Missense Variants Affecting Carcass Traits for Hanwoo Precision Breeding. Genes (Basel) 2023; 14:1839. [PMID: 37895191 PMCID: PMC10606632 DOI: 10.3390/genes14101839] [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] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
This study aimed to identify causal variants associated with important carcass traits such as weight and meat quality in Hanwoo cattle. We analyzed missense mutations extracted from imputed sequence data (ARS-UCD1.2) and performed an exon-specific association test on the carcass traits of 16,970 commercial Hanwoo. We found 33, 2, 1, and 3 significant SNPs associated with carcass weight (CW), backfat thickness (BFT), eye muscle area (EMA), and marbling score (MS), respectively. In CW and EMA, the most significant missense SNP was identified at 19,524,263 on BTA14 and involved the PRKDC. A missense SNP in the ZFAND2B, located at 107,160,304 on BTA2 was identified as being involved in BFT. For MS, missense SNP in the ACVR2B gene, located at 11,849,704 in BTA22 was identified as the most significant marker. The contribution of the most significant missense SNPs to genetic variance was confirmed to be 8.47%, 2.08%, 1.73%, and 1.19% in CW, BFT, EMA, and MS, respectively. We generated favorable and unfavorable haplotype combinations based on the significant SNPs for CW. Significant differences in GEBV (Genomic Estimated Breeding Values) were observed between groups with each favorable and unfavorable haplotype combination. In particular, the missense SNPs in PRKDC, MRPL9, and ANKFN1 appear to significantly affect the protein's function and structure, making them strong candidates as causal mutations. These missense SNPs have the potential to serve as valuable markers for improving carcass traits in Hanwoo commercial farms.
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Affiliation(s)
- Dong Jae Lee
- Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea; (D.J.L.); (Y.C.); (D.L.); (S.H.L.)
| | - Yoonsik Kim
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Republic of Korea; (Y.K.); (P.T.N.D.)
| | - Phuong Thanh N. Dinh
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Republic of Korea; (Y.K.); (P.T.N.D.)
| | - Yoonji Chung
- Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea; (D.J.L.); (Y.C.); (D.L.); (S.H.L.)
| | - Dooho Lee
- Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea; (D.J.L.); (Y.C.); (D.L.); (S.H.L.)
| | - Yeongkuk Kim
- Quantomic Research & Solution, Daejeon 34134, Republic of Korea;
| | - Soo Hyun Lee
- Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea; (D.J.L.); (Y.C.); (D.L.); (S.H.L.)
| | - Inchul Choi
- Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Republic of Korea; (D.J.L.); (Y.C.); (D.L.); (S.H.L.)
| | - Seung Hwan Lee
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Republic of Korea; (Y.K.); (P.T.N.D.)
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Li S, Zhang W, Liang P, Zhu M, Zheng B, Zhou W, Wang C, Zhao X. Novel variants in the CLCN4 gene associated with syndromic X-linked intellectual disability. Front Neurol 2023; 14:1096969. [PMID: 37789889 PMCID: PMC10542403 DOI: 10.3389/fneur.2023.1096969] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 08/15/2023] [Indexed: 10/05/2023] Open
Abstract
Objective The dysfunction of the CLCN4 gene can lead to X-linked intellectual disability and Raynaud-Claes syndrome (MRXSRC), characterized by severe cognitive impairment and mental disorders. This study aimed to investigate the genetic defects and clinical features of Chinese children with CLCN4 variants and explore the effect of mutant ClC-4 on the protein expression level and subcellular localization through in vitro experiments. Methods A total of 401 children with intellectual disabilities were screened for genetic variability using whole-exome sequencing (WES). Clinical data, including age, sex, perinatal conditions, and environmental exposure, were collected. Cognitive, verbal, motor, and social behavioral abilities were evaluated. Candidate variants were verified using Sanger sequencing, and their pathogenicity and conservation were analyzed using in silico prediction tools. Protein expression and localization of mutant ClC-4 were measured using Western blotting (WB) and immunofluorescence microscopy. The impact of a splice site variant was assessed with a minigene assay. Results Exome analysis identified five rare CLCN4 variants in six unrelated patients with intellectual disabilities, including two recurrent heterozygous de novo missense variants (p.D89N and p.A555V) in three female patients, and two hemizygous missense variants (p.N141S and p.R694Q) and a splicing variant (c.1390-12T > G) that are maternally inherited in three male patients. The p.N141S variant and the splicing variant c.1390-12(T > G were novel, while p.R694Q was identified in two asymptomatic heterozygous female patients. The six children with CLCN4 variants exhibited a neurodevelopmental spectrum disease characterized by intellectual disability (ID), delayed speech, autism spectrum disorders (ASD), microcephaly, hypertonia, and abnormal imaging findings. The minigene splicing result indicated that the c.1390-12T > G did not affect the splicing of CLCN4 mRNA. In vitro experiments showed that the mutant protein level and localization of mutant protein are similar to the wild type. Conclusion The study identified six probands with CLCN4 gene variants associated with X-linked ID. It expanded the gene and phenotype spectrum of CLCN4 variants. The bioinformatic analysis supported the pathogenicity of CLCN4 variants. However, these CLCN4 gene variants did not affect the ClC-4 expression levels and protein location, consistent with previous studies. Further investigations are necessary to investigate the pathogenetic mechanism.
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Affiliation(s)
- Sinan Li
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Wenxin Zhang
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Piao Liang
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Min Zhu
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Bixia Zheng
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Zhou
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Chunli Wang
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoke Zhao
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, Nanjing, China
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Al Ali J, Yang J, Phillips MS, Fink J, Mastrianni J, Seibert K. A case report of a patient with primary familial brain calcification with a PDGFRB genetic variant. Front Neurol 2023; 14:1235909. [PMID: 37780723 PMCID: PMC10538541 DOI: 10.3389/fneur.2023.1235909] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023] Open
Abstract
Fahr's disease, or primary familial brain calcification (PFBC), is a rare genetic neurologic disease characterized by abnormal calcification of the basal ganglia, subcortical white matter and cerebellum. Common clinical features include parkinsonism, neuropsychiatric symptoms, and cognitive decline. Genes implicated in Fahr's disease include PDGFB, PDGFRB, SLC20A2, XPR1, MYORG, and JAM2. We present the case of a 51-year-old woman who developed subacute cognitive and behavioral changes primarily affecting frontal-subcortical pathways and parkinsonism in association with extensive bilateral calcifications within the basal ganglia, subcortical white matter, and cerebellum on neuroimaging. Relevant family history included a paternal aunt with parkinsonism at age 50. Normal parathyroid hormone and calcium levels in the patient's serum ruled out hypoparathyroidism or pseudohypoparathyroidism as causes for the intracranial calcifications. Genetic panel sequencing revealed a variant of unknown significance in the PDGFRB gene resulting in a p.Arg919Gln substitution in the tyrosine kinase domain of PDGFRB protein. To our knowledge this is the first report of a p.Arg919Gln variant in the PDGFRB gene associated with PFBC. Although co-segregation studies were not possible in this family, the location of the variant is within the tyrosine kinase domain of PDGFRB and pathogenicity calculators predict it is likely to be pathogenic. This report adds to the list of genetic variants that warrant functional analysis and could underlie the development of PFBC, which may help to further our understanding of its pathogenesis and the development of targeted therapies for this disorder.
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Affiliation(s)
- Jamal Al Ali
- Department of Neurology, University of Chicago, Chicago, IL, United States
| | - Jessica Yang
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, United States
| | - Matthew S. Phillips
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, United States
| | - Joseph Fink
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, United States
| | - James Mastrianni
- Department of Neurology, University of Chicago, Chicago, IL, United States
| | - Kaitlin Seibert
- Department of Neurology, University of Chicago, Chicago, IL, United States
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17
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Yin L, Zhu Y, Jiang W, Song Y, Lu Y, Tao D, Liu Y, Ma Y. Functional characterization of a rare pathogenic variant c.875G > A, p.(Cys292Tyr) in COMP. Ann Hum Genet 2023; 87:241-247. [PMID: 37461830 DOI: 10.1111/ahg.12521] [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] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND The protein encoded by the cartilage oligomeric matrix protein (COMP) gene is a noncollagenous extracellular matrix (ECM) protein that is important for chondrocyte formation and growth. Variations in the COMP gene cause pseudoachondroplasia (PSACH), which is mainly characterized by short-limbed dwarfing in the clinic. AIMS To characterize the function of a rare pathogenic variant in the COMP gene (c.875G > A, p.Cys292Tyr). MATERIALS & METHODS We performed 3D structural analysis, in vitro expression analysis, and immunofluorescence to characterize the effects of the variant on protein structure, expression, and cellular localization respectively. RESULTS Variation modeling showed that the interactions between amino acids were changed after the variation, and there were 31 changes in the secondary structure of mutant COMP (MT-COMP). Western blot showed that the intracellular quantity of MT-COMP was higher than the wild-type COMP (WT-COMP). Cellular immunofluorescence results showed that WT-COMP was less abundant and homogenously distributed in cells, while the MT-COMP accumulated in the cytoplasm. DISCUSSION Herein, we report a variant of COMP in a Chinese family with PSACH. We have shown that the rare missense variant, COMP c.875G > A, previously reported in ClinVar and identified in our patient, results in excessive accumulation of mutant protein in the cytoplasm, and is therefore pathogenic. CONCLUSION Through in silico and experimental analyses, we provide evidence that COMP c.875G > A is the likely cause of PSACH in a Chinese family.
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Affiliation(s)
- Lan Yin
- Department of Medical Genetics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yingchuan Zhu
- Department of Medical Genetics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wenhao Jiang
- Department of Medical Genetics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yue Song
- Department of Medical Genetics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yilu Lu
- Department of Medical Genetics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Dachang Tao
- Department of Medical Genetics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yunqiang Liu
- Department of Medical Genetics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yongxin Ma
- Department of Medical Genetics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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18
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Marutani S, Nishino T, Shimokawa O, Pooh RK, Morisaki H, Inamura N. Aortic Dissection and a Previously Unreported ACTA2 Missense Variant Mutation in a Young Patient: A Case Report. Pediatr Dev Pathol 2023; 26:494-498. [PMID: 37672683 DOI: 10.1177/10935266231194701] [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] [Indexed: 09/08/2023]
Abstract
Hereditary connective tissue disease is known to cause aortic lesions at an early age. Familial aortic aneurysm/dissection is caused due to an ACTA2 mutation that affects smooth muscle structure. We present a case of a 15-year-old boy with a mild developmental disorder in whom no abnormalities were identified on previous physical examinations. The patient presented with severe left heart failure, extensive dissection from the ascending aorta to the common iliac artery, and myocardial and cerebral infarctions. He underwent an urgent Bentall surgery. Six months later, the patient underwent surgical reconstruction of the abdominal aorta from the aortic arch and returned to normal daily activities. Pathological examination demonstrated the absence of elastic fibers but presence of abundant reticular fibers and mucopolysaccharides from the tunica intima to the media. Genetic testing revealed a heterozygous missense variant of the ACTA2 gene. To the best of our knowledge, this is the first sporadic case of structurally abnormal smooth muscle organization resulting in clinical symptoms with no previously reported pathogenicity.
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Affiliation(s)
- Satoshi Marutani
- Department of Pediatrics, Faculty of Medicine, Kindai University, Osakasayama City, Osaka, Japan
| | - Takako Nishino
- Department of Cardiovascular Surgery, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Osamu Shimokawa
- Clinical Laboratory, Ritz Medical Co., Ltd., Tennoji, Osaka, Japan
| | | | - Hiroko Morisaki
- Department of Medical Genetics, Sakakibara Heart Institute, Fuchucity, Tokyo, Japan
| | - Noburu Inamura
- Department of Pediatrics, Faculty of Medicine, Kindai University, Osakasayama City, Osaka, Japan
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19
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Li L, Yuan L, Zheng W, Yang Y, Deng X, Song Z, Deng H. An SCN1A gene missense variant in a Chinese Tujia ethnic family with genetic epilepsy with febrile seizures plus. Front Neurol 2023; 14:1229569. [PMID: 37576022 PMCID: PMC10412811 DOI: 10.3389/fneur.2023.1229569] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 06/30/2023] [Indexed: 08/15/2023] Open
Abstract
Genetic epilepsy with febrile seizures plus (GEFSP) is a familial epileptic syndrome that is genetically heterogeneous and inherited in an autosomal dominant form in most cases. To date, at least seven genes have been reported to associate with GEFSP. This study aimed to identify the disease-causing variant in a Chinese Tujia ethnic family with GEFSP by using whole exome sequencing, Sanger sequencing, and in silico prediction. A heterozygous missense variant c.5725A>G (p.T1909A) was identified in the sodium voltage-gated channel alpha subunit 1 gene (SCN1A) coding region. The variant co-segregated with the GEFSP phenotype in this family, and it was predicted as disease-causing by multiple in silico programs, which was proposed as the genetic cause of GEFSP, further genetically diagnosed as GEFSP2. These findings expand the genetic and phenotypic spectrum of GEFSP and should contribute to genetic diagnoses, personalized therapies, and prognoses.
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Affiliation(s)
- Ling Li
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Lamei Yuan
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
- Disease Genome Research Center, Central South University, Changsha, China
| | - Wen Zheng
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yan Yang
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xiong Deng
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhi Song
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hao Deng
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
- Disease Genome Research Center, Central South University, Changsha, China
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20
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Yuan Y, Yan D, Skidmore J, Chapagain P, Liu X, He S. Responsiveness of the electrically stimulated cochlear nerve in patients with a missense variant in ACTG1: Preliminary Results. Front Audiol Otol 2023; 1:1213323. [PMID: 38590973 PMCID: PMC11000624 DOI: 10.3389/fauot.2023.1213323] [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] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
This preliminary study identified a missense variant in ACTG1 (NM_001614.5) in a family with autosomal dominant non-syndromic hearing loss (ADNSHL). The responsiveness of the electrically-stimulated cochlear nerve (CN) in two implanted participants with this missense change was also evaluated and reported. Genetic testing was done using a custom capture panel (MiamiOtoGenes) and whole exome sequencing. The responsiveness of the electrically-stimulated CN was evaluated in two members of this family (G1 and G4) using the electrically evoked compound action potential (eCAP). eCAP results from these two participants were compared with those measured three implanted patient populations: children with cochlear nerve deficiency, children with idiopathic hearing loss and normal-sized cochlear nerves, and postligually deafened adults. Sequencing of ACTG1 identified a missense c.737A>T (p. Gln246Leu) variant in ACTG1 (NM_001614.5) which is most likely the genetic cause of ADNSHL in this family. eCAP results measured in these two participants showed substantial variations. The results indicated the missense c.737A>T (p. Gln246Leu) variant in ACTG1 (NM_001614.5) co-segregated with hearing loss in this family. The responsiveness of the electrically-stimulated CN can vary among patients with the same genetic variants, which suggests the importance of evaluating the functional status of the CN for individual CI patients.
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Affiliation(s)
- Yi Yuan
- Department of Otolaryngology – Head & Neck Surgery, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Denise Yan
- Department of Otolaryngology – Head & Neck Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Jeffrey Skidmore
- Department of Otolaryngology – Head & Neck Surgery, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Prem Chapagain
- Department of Physics and Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA
| | - Xuezhong Liu
- Department of Otolaryngology – Head & Neck Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA
- Dr. John T. MacDonald Foundation, Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Shuman He
- Department of Otolaryngology – Head & Neck Surgery, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
- Department of Audiology, Nationwide Children’s Hospital, Columbus, Ohio, USA
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21
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Ramakrishnan G, Baakman C, Heijl S, Vroling B, van Horck R, Hiraki J, Xue LC, Huynen MA. Understanding structure-guided variant effect predictions using 3D convolutional neural networks. Front Mol Biosci 2023; 10:1204157. [PMID: 37475887 PMCID: PMC10354367 DOI: 10.3389/fmolb.2023.1204157] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/22/2023] [Indexed: 07/22/2023] Open
Abstract
Predicting pathogenicity of missense variants in molecular diagnostics remains a challenge despite the available wealth of data, such as evolutionary information, and the wealth of tools to integrate that data. We describe DeepRank-Mut, a configurable framework designed to extract and learn from physicochemically relevant features of amino acids surrounding missense variants in 3D space. For each variant, various atomic and residue-level features are extracted from its structural environment, including sequence conservation scores of the surrounding amino acids, and stored in multi-channel 3D voxel grids which are then used to train a 3D convolutional neural network (3D-CNN). The resultant model gives a probabilistic estimate of whether a given input variant is disease-causing or benign. We find that the performance of our 3D-CNN model, on independent test datasets, is comparable to other widely used resources which also combine sequence and structural features. Based on the 10-fold cross-validation experiments, we achieve an average accuracy of 0.77 on the independent test datasets. We discuss the contribution of the variant neighborhood in the model's predictive power, in addition to the impact of individual features on the model's performance. Two key features: evolutionary information of residues in the variant neighborhood and their solvent accessibilities were observed to influence the predictions. We also highlight how predictions are impacted by the underlying disease mechanisms of missense mutations and offer insights into understanding these to improve pathogenicity predictions. Our study presents aspects to take into consideration when adopting deep learning approaches for protein structure-guided pathogenicity predictions.
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Affiliation(s)
- Gayatri Ramakrishnan
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Coos Baakman
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, Netherlands
| | | | | | | | | | - Li C. Xue
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Martijn A. Huynen
- Department of Medical Biosciences, Radboud University Medical Center, Nijmegen, Netherlands
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22
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Miura S, Hiruki S, Okada T, Takei SI, Senzaki K, Okada Y, Ochi M, Tanabe Y, Ochi H, Igase M, Ohyagi Y, Shibata H. Case report: Frontotemporal dementia and amyotrophic lateral sclerosis caused by a missense variant (p.Arg89Trp) in the valosin-containing protein gene. Front Genet 2023; 14:1155998. [PMID: 37303947 PMCID: PMC10250589 DOI: 10.3389/fgene.2023.1155998] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/12/2023] [Indexed: 06/13/2023] Open
Abstract
Frontotemporal dementia and/or amyotrophic lateral sclerosis 6, also known as amyotrophic lateral sclerosis 14, is an autosomal dominant, progressive neurodegenerative disorder caused by various mutations in the valosin-containing protein gene. In this report, we examined a 51-year-old female Japanese patient with frontotemporal dementia and amyotrophic lateral sclerosis. The patient began noticing gait disturbances at the age of 45 years. Neurological examination at the age of 46 years met the Awaji criteria for clinically probable amyotrophic lateral sclerosis. At the age of 49 years, she tended to have poor mood and an aversion to activity. Her symptoms gradually worsened. She required a wheelchair for transport and had difficulty communicating with others because of poor comprehension. She then began to frequently exhibit irritability. Eventually, she was admitted to the psychiatric hospital because uncontrollable violent behavior throughout the day. Longitudinal brain magnetic resonance imaging revealed progressive brain atrophy with temporal dominance, non-progressive cerebellar atrophy, and some non-specific white matter intensities. Brain single photon emission computed tomography showed hypoperfusion in the bilateral temporal lobes and cerebellar hemispheres. Clinical exome sequencing revealed the presence of a heterozygous nonsynonymous variant (NM_007126.5, c.265C>T; p.Arg89Trp) in the valosin-containing protein gene, which was absent in the 1000 Genomes Project, the Exome Aggregation Consortium Database, and the Genome Aggregation Database, and was predicted to be "damaging" by PolyPhen-2 and "deleterious" using SIFT with a Combined Annotation Dependent Depletion score of 35. We also confirmed the absence of this variant in 505 Japanese control subjects. Therefore, we concluded that the variant in the valosin-containing protein gene was responsible for the symptoms of this patient.
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Affiliation(s)
- Shiroh Miura
- Department of Neurology and Geriatric Medicine, Ehime University Graduate School of Medicine, Toon, Ehime, Japan
| | - Shigeyoshi Hiruki
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Tomohisa Okada
- Department of Radiology, Ehime University Graduate School of Medicine, Toon, Ehime, Japan
| | - Satoko Itani Takei
- Department of Neurology and Geriatric Medicine, Ehime University Graduate School of Medicine, Toon, Ehime, Japan
| | - Kensuke Senzaki
- Department of Neurology and Geriatric Medicine, Ehime University Graduate School of Medicine, Toon, Ehime, Japan
| | - Yoko Okada
- Department of Neurology and Geriatric Medicine, Ehime University Graduate School of Medicine, Toon, Ehime, Japan
| | - Masayuki Ochi
- Department of Neurology and Geriatric Medicine, Ehime University Graduate School of Medicine, Toon, Ehime, Japan
| | - Yuki Tanabe
- Department of Radiology, Ehime University Graduate School of Medicine, Toon, Ehime, Japan
| | - Hirofumi Ochi
- Department of Intractable Disease and Aging Science, Ehime University Graduate School of Medicine, Toon, Ehime, Japan
| | - Michiya Igase
- Department of Anti-aging Medicine, Ehime University Graduate School of Medicine, Toon, Ehime, Japan
| | - Yasumasa Ohyagi
- Department of Neurology and Geriatric Medicine, Ehime University Graduate School of Medicine, Toon, Ehime, Japan
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
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23
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Kittock CM, Saifeddine M, Straight L, Ward DI. U2AF2 variant in a patient with developmental delay, dysmorphic features, and epilepsy. Am J Med Genet A 2023. [PMID: 37092751 DOI: 10.1002/ajmg.a.63221] [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: 02/01/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/25/2023]
Abstract
Variants in the RNA binding protein (RBP) U2AF2 are hypothesized to cause a novel neurodevelopmental disorder. Here, we report a patient with a de novo missense variant in U2AF2, the second case report of the same variant, and third case report overall. The patient in this report has a history of global developmental delay, dysmorphic features, and epilepsy. This presentation is consistent with the previous case report with the same U2AF2 variant and with a recent case report of another U2AF2 variant, strengthening the evidence that variants in U2AF2 are the cause of a novel neurodevelopmental disorder.
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Affiliation(s)
- Claire M Kittock
- Department of Pediatrics, University of South Dakota Sanford School of Medicine, Sioux Falls, South Dakota, USA
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, South Dakota, USA
| | - Mohamad Saifeddine
- Department of Pediatrics, University of South Dakota Sanford School of Medicine, Sioux Falls, South Dakota, USA
- Sanford Children's Specialty Clinic, Sioux Falls, South Dakota, USA
| | - Lisa Straight
- Department of Pediatrics, University of South Dakota Sanford School of Medicine, Sioux Falls, South Dakota, USA
- Sanford Children's Specialty Clinic, Sioux Falls, South Dakota, USA
| | - D Isum Ward
- Department of Pediatrics, University of South Dakota Sanford School of Medicine, Sioux Falls, South Dakota, USA
- Sanford Children's Specialty Clinic, Sioux Falls, South Dakota, USA
- Sanford Imagenetics, Sioux Falls, South Dakota, USA
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24
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Cevik S, Biswas SB, Biswas-Fiss EE. Structural and Pathogenic Impacts of ABCA4 Variants in Retinal Degenerations-An In-Silico Study. Int J Mol Sci 2023; 24:ijms24087280. [PMID: 37108442 PMCID: PMC10138569 DOI: 10.3390/ijms24087280] [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] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The retina-specific ATP-binding cassette transporter protein ABCA4 is responsible for properly continuing the visual cycle by removing toxic retinoid byproducts of phototransduction. Functional impairment caused by ABCA4 sequence variations is the leading cause of autosomal recessive inherited retinal disorders, including Stargardt disease, retinitis pigmentosa, and cone-rod dystrophy. To date, more than 3000 ABCA4 genetic variants have been identified, approximately 40 percent of which have not been able to be classified for pathogenicity assessments. This study examined 30 missense ABCA4 variants using AlphaFold2 protein modeling and computational structure analysis for pathogenicity prediction. All variants classified as pathogenic (n = 10) were found to have deleterious structural consequences. Eight of the ten benign variants were structurally neutral, while the remaining two resulted in mild structural changes. This study's results provided multiple lines of computational pathogenicity evidence for eight ABCA4 variants of uncertain clinical significance. Overall, in silico analyses of ABCA4 can provide a valuable tool for understanding the molecular mechanisms of retinal degeneration and their pathogenic impact.
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Affiliation(s)
- Senem Cevik
- Department of Medical and Molecular Sciences, College of Health Sciences, University of Delaware, 16 West Main Street, Suite 302 WHL, Newark, DE 19716, USA
- Ammon Pinizzotto Biopharmaceutical Innovation Center, 590 Avenue 1743, Newark, DE 19713, USA
| | - Subhasis B Biswas
- Department of Medical and Molecular Sciences, College of Health Sciences, University of Delaware, 16 West Main Street, Suite 302 WHL, Newark, DE 19716, USA
- Ammon Pinizzotto Biopharmaceutical Innovation Center, 590 Avenue 1743, Newark, DE 19713, USA
| | - Esther E Biswas-Fiss
- Department of Medical and Molecular Sciences, College of Health Sciences, University of Delaware, 16 West Main Street, Suite 302 WHL, Newark, DE 19716, USA
- Ammon Pinizzotto Biopharmaceutical Innovation Center, 590 Avenue 1743, Newark, DE 19713, USA
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25
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Zhang X, Kang X, Yang M, Cai Z, Song Y, Zhou X, Cao J, Wang C, Huang K, Peng Y, He J, Xiao Z. A variant of RAG1 gene identified in severe combined immunodeficiency: a case report. BMC Pediatr 2023; 23:56. [PMID: 36732712 PMCID: PMC9896705 DOI: 10.1186/s12887-022-03822-0] [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] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/24/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The recombination-activating gene 1 (RAG1) protein is essential for the V (variable)-D (diversity)-J (joining) recombination process. Mutations in RAG1 have been reported to be associated with several types of immune disorders. Typical clinical features driven by RAG1 variants include persistent infections, severe lymphopenia, and decreased immunoglobulin levels . CASE PRESENTATION In this study, a 2-month-24-days-old infant with recurrent fever was admitted to our hospital with multiple infections and absence of T and B lymphocytes. The infant was diagnosed with severe combined immunodeficiency (SCID). A homozygous variation c.2147G>A (NM_000448.2: exonme2: c.2147G>A (p.Arg716Gln)) was identified in the RAG1 gene using whole-exome sequencing and Sanger sequencing. The predicted 3D structure of variant RAG1 indicated altered protein stability. Additionally, decreased expression of variant RAG1 gene was detected at both the mRNA and protein levels. CONCLUSIONS Our study identified a novel homozygous variant in RAG1 gene that causes SCID. This finding expands the variant spectrum of RAG1 in SCID and provides further evidence for the clinical diagnosis of SCID.
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Affiliation(s)
- Xinping Zhang
- grid.440223.30000 0004 1772 5147Department of Pediatric Intensive Care Unit of Hunan Children’s Hospital, Changsha, Hunan People’s Republic of China
| | - Xiayan Kang
- grid.440223.30000 0004 1772 5147Department of Pediatric Intensive Care Unit of Hunan Children’s Hospital, Changsha, Hunan People’s Republic of China
| | - Meiyu Yang
- grid.440223.30000 0004 1772 5147Department of Pediatric Intensive Care Unit of Hunan Children’s Hospital, Changsha, Hunan People’s Republic of China
| | - Zili Cai
- grid.440223.30000 0004 1772 5147Department of Pediatric Intensive Care Unit of Hunan Children’s Hospital, Changsha, Hunan People’s Republic of China
| | - Yulei Song
- grid.440223.30000 0004 1772 5147Department of Pediatric Intensive Care Unit of Hunan Children’s Hospital, Changsha, Hunan People’s Republic of China
| | - Xiong Zhou
- grid.440223.30000 0004 1772 5147Department of Pediatric Intensive Care Unit of Hunan Children’s Hospital, Changsha, Hunan People’s Republic of China
| | - Jianshe Cao
- grid.440223.30000 0004 1772 5147Department of Pediatric Intensive Care Unit of Hunan Children’s Hospital, Changsha, Hunan People’s Republic of China
| | - Chengjuan Wang
- grid.440223.30000 0004 1772 5147Department of Pediatric Intensive Care Unit of Hunan Children’s Hospital, Changsha, Hunan People’s Republic of China
| | - Kang Huang
- grid.440223.30000 0004 1772 5147Department of Pediatric Intensive Care Unit of Hunan Children’s Hospital, Changsha, Hunan People’s Republic of China
| | - Yani Peng
- grid.440223.30000 0004 1772 5147Department of Pediatric Intensive Care Unit of Hunan Children’s Hospital, Changsha, Hunan People’s Republic of China
| | - Jie He
- grid.440223.30000 0004 1772 5147Department of Pediatric Intensive Care Unit of Hunan Children’s Hospital, Changsha, Hunan People’s Republic of China
| | - Zhenghui Xiao
- Department of Pediatric Intensive Care Unit of Hunan Children's Hospital, Changsha, Hunan, People's Republic of China.
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26
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Shi J, Xu K, Zhang X, Xie Y, Chang H, Li Y. A novel missense ALMS1 variant causes aberrant splicing identified in a cohort of patients with Alström syndrome. Front Genet 2023; 13:1104420. [PMID: 36685911 PMCID: PMC9845408 DOI: 10.3389/fgene.2022.1104420] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/12/2022] [Indexed: 01/05/2023] Open
Abstract
Purpose: Alström syndrome (AS) is a rare autosomal recessive disorder caused by variants of ALMS1. The objectives of this study were to describe the clinical and genetic characteristics of 19 Chinese patients with biallelic variants in ALMS1. Methods: We recruited 19 probands with biallelic disease-causing ALMS1 variants. All patients underwent ophthalmic and systematic evaluations and comprehensive molecular genetic analysis. Reverse transcriptase-polymerase chain reaction (RT-PCR) assays were performed to observe the effect of a novel missense variant on ALMS1 pre-mRNA splicing. Results: We identified 33 causative variants in ALMS1, including 15 frameshift small indels, 14 non-sense variants, two gross deletions, one splicing variant, and one missense variant. RT-PCR showed that the missense variant c.9542G>A (p.R3181Q) altered pre-mRNA splicing to generate a truncated protein p. (Ser3082Asnfs*6). Retinal dystrophy (RD) was noted in all the patients, followed by metabolism disturbance (obesity or acanthosis nigricans) in 66.7% and hearing impairment in 61.1% of the patients. Patient systemic symptom numbers and their age at evaluation showed a significant positive correlation, and BCVA and age at the last examination showed a moderate correlation. All patients exhibited early-onset RD and severe visual impairment. The exception was one patient carrying homozygous p. R3181Q, who showed a mild visual defect and atypical retinal phenotype. Conclusion: Our findings expand the pathogenic variant spectrum of ALMS1 and provide the first verification of a novel missense variant caused AS by aberrant pre-mRNA splicing. Patients with AS might demonstrate varied clinical spectra; therefore, genetic analysis is vital for the early and accurate diagnosis of patients with atypical AS.
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27
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Chen Y, Yang X, Yan X, Shen L, Guo J, Xu Q. A novel SEMA6B variant causes adult-onset progressive myoclonic epilepsy-11 in a Chinese family: A case report and literature review. Front Genet 2023; 14:1110310. [PMID: 36873942 PMCID: PMC9974634 DOI: 10.3389/fgene.2023.1110310] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/26/2023] [Indexed: 02/17/2023] Open
Abstract
This study describes a patient with progressive myoclonic epilepsy-11 (EPM-11), which follows autosomal dominant inheritance caused by a novel SEMA6B variant. Most patients develop this disease during infancy or adolescence with action myoclonus, generalized tonic-clonic seizures (GTCS), and progressive neurological deterioration. No cases of adult-onset EPM-11 have been reported yet. Here, we present one case of adult-onset EPM-11 who experienced gait instability, seizures, and cognitive impairment, and harbored a novel missense variant, c.432C>G (p.C144W). Our findings provide a foundation for a better understanding of the phenotypic and genotypic profiles of EPM-11. Further functional studies are recommended to elucidate the pathogenesis of this disease.
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Affiliation(s)
- Yirao Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xingyan Yang
- Department of Neurology, Central Hospital, Bai Yin, China
| | - Xinxiang Yan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China.,Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
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28
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Gruber LM, Hart SN, Maher Iii LJ. Succinate dehydrogenase variants in paraganglioma: why are B subunit variants 'bad'? Endocr Oncol 2023; 3:e220093. [PMID: 37434649 PMCID: PMC10305465 DOI: 10.1530/eo-22-0093] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 07/13/2023]
Abstract
Mutations that predispose to familial pheochromocytoma and paraganglioma include inherited variants in the four genes (SDHA, SDHB, SDHC and SDHD) encoding subunits of succinate dehydrogenase (SDH), an enzyme of the mitochondrial tricarboxylic acid cycle and complex II of the electron transport chain. In heterozygous variant carriers, somatic loss of heterozygosity is thought to result in tumorigenic accumulation of succinate and reactive oxygen species. Inexplicably, variants affecting the SDHB subunit predict worse clinical outcomes. Why? Here we consider two hypotheses. First, relative to SDH A, C and D subunits, the small SDHB subunit might be more intrinsically 'fragile' to missense mutations because of its relatively large fraction of amino acids contacting prosthetic groups and other SDH subunits. We show evidence that supports this hypothesis. Second, the natural pool of human SDHB variants might, by chance, be biased toward severe truncating variants and missense variants causing more disruptive amino acid substitutions. We tested this hypothesis by creating a database of known SDH variants and predicting their biochemical severities. Our data suggest that natural SDHB variants are more pathogenic. It is unclear if this bias is sufficient to explain clinical data. Other explanations include the possibility that SDH subcomplexes remaining after SDHB loss have unique tumorigenic gain-of-function characteristics, and/or that SDHB may have additional unknown tumor-suppressor functions.
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Affiliation(s)
- Lucinda M Gruber
- Division of Endocrinology, Mayo Clinic, Rochester, Minnesota, USA
| | - Steven N Hart
- Department of Computational Pathology and Artificial Intelligence, Mayo Clinic, Rochester, Minnesota, USA
| | - Louis James Maher Iii
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
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29
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Verhoeven W, Zuijdam J, Scheick A, van Nieuwenhuijsen F, Zwemer AS, Pfundt R, Egger J. Myoclonic-Atonic Epilepsy Caused by a Novel de Novo Heterozygous Missense Variant in the SLC6A1 Gene: Brief Discussion of the Literature and Detailed Case Description of a Severely Intellectually Disabled Adult Male Patient. Int Med Case Rep J 2022; 15:753-759. [PMID: 36582431 PMCID: PMC9793742 DOI: 10.2147/imcrj.s390636] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/10/2022] [Indexed: 12/25/2022] Open
Abstract
Introduction Diagnostic exome sequencing has yielded over the past decades a great number of molecular diagnoses for genetic disorders in which both intellectual disability and epilepsy are present. One of these syndromes is myoclonic-atonic epilepsy (MAE) that is caused by pathogenic variants in the SLC6A1 gene located at 3p25.3. The most relevant clinical characteristics are intellectual disability, several forms of mostly treatment-resistant epilepsy starting at young age, serious disinhibitory behavioural problems, language impairment, higher pain tolerance, and symptoms from the autism spectrum, all in the absence of any consistent dysmorphism or malformation. Methods After an overview of the literature, here, the developmental trajectory of a 55-year-old severely intellectually disabled male with therapy-resistant epilepsy and aggressive outburst is reported in detail, in whom no etiological diagnosis had been performed. Next to genetic, neurological, and neuropsychiatric examination, psychological assessment with validated instruments was performed. Results Exome sequencing and targeted analysis of the patient and both his parents demonstrated a de novo missense variant in the SLC6A1 gene which was never before described in the literature nor in control databases. The phenotypical presentation of the patient with treatment-resistant epilepsy, especially absences and myoclonic seizures, as well as sleep disturbances and autism, corresponds with a diagnosis of MAE. Discussion This case stresses that exome sequencing should be the first-tier diagnostic test for patients with unexplained neurodevelopmental disorders, regardless of their age, and that as yet the most suitable approach is the formation of an interdisciplinary team for treatment design and clinical management.
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Affiliation(s)
- Willem Verhoeven
- Department of Psychiatry, Erasmus University Medical Center, Rotterdam, the Netherlands,Centre for Consultation and Expertise, Utrecht, the Netherlands,Vincent van Gogh Centre of Excellence for Neuropsychiatry, Venray, the Netherlands,Correspondence: Willem Verhoeven, Centre of Excellence for Neuropsychiatry, Stationsweg 46, Venray, 5803 AC, the Netherlands, Tel +31651156556, Fax +31478584765, Email
| | - José Zuijdam
- Raphael Institute Breidablick, Centre for People with Intellectual Disabilities, Middenbeemster, the Netherlands
| | - Anneke Scheick
- Raphael Institute Breidablick, Centre for People with Intellectual Disabilities, Middenbeemster, the Netherlands
| | | | - Anne-Suus Zwemer
- ASVZ, Centre for People with Intellectual Disabilities, Sliedrecht, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
| | - Jos Egger
- Vincent van Gogh Centre of Excellence for Neuropsychiatry, Venray, the Netherlands,Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, the Netherlands
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30
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Zhao X, Gao C, Li L, Jiang L, Wei Y, Che F, Liu Q. Clinical Exome Sequencing Identifies NDP Gene Variants in Two Chinese Families with X-Linked Norrie Disease. Genet Test Mol Biomarkers 2022; 26:589-594. [PMID: 36577125 DOI: 10.1089/gtmb.2022.0142] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Purpose: To explore the genetic defects in two Chinese families with X-linked Norrie disease (ND). Methods: We analyzed two Chinese families with ND at molecular level through clinical exome sequencing and the variations were identified by Sanger sequencing. Results: Two genetic variations were found in the NDP gene by clinical exome sequencing, a partial deletion of 801 bp contained the whole exon 2 and a missense variant (164G>A) within codon 55 that resulted in the interchange of cysteine by phenylalanine. Clinical findings were more severe in the patients who presented the missense variant. Conclusion: We report two genetic variations in the NDP gene in Chinese that extend the mutational and phenotypic spectra of NDP gene, and also demonstrate the feasibility of clinical exome sequencing in application of molecular diagnosis.
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Affiliation(s)
- Xiangyu Zhao
- Department of Laboratory Medicine, Linyi People's Hospital, Shandong University, Linyi, China.,Key Laboratory for Laboratory Medicine of Linyi City, Linyi, China
| | - Chunhai Gao
- Department of Laboratory Medicine, Linyi People's Hospital, Shandong University, Linyi, China.,Key Laboratory for Laboratory Medicine of Linyi City, Linyi, China
| | - Lin Li
- Department of Laboratory Medicine, Linyi People's Hospital, Shandong University, Linyi, China.,Key Laboratory for Laboratory Medicine of Linyi City, Linyi, China
| | - Liangqian Jiang
- Department of Laboratory Medicine, Linyi People's Hospital, Shandong University, Linyi, China.,Key Laboratory for Laboratory Medicine of Linyi City, Linyi, China
| | - Yuda Wei
- Department of Laboratory Medicine, Linyi People's Hospital, Shandong University, Linyi, China.,Key Laboratory for Laboratory Medicine of Linyi City, Linyi, China
| | - Fengyuan Che
- Department of Central Laboratory, Linyi People's Hospital, Shandong University, Linyi, China.,Department of Neurology, Linyi People's Hospital, Shandong University, Linyi, China
| | - Qiji Liu
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
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31
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Gochenauer AE, Dreger DL, Davis BW, Cook S, Barber KE, Ekenstedt KJ. ABCG2 Polymorphisms and Predictive Fluoroquinolone Phototoxicity in Nondomestic Felids. Genes (Basel) 2022; 13. [PMID: 36553444 DOI: 10.3390/genes13122178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
Fluoroquinolones are a widely used class of chemotherapeutics within veterinary medicine, prized for their broad-spectrum bactericidal activity. These drugs present a known risk of retinal phototoxicity in domestic cats (Felis catus); therefore, using lower doses and alternative antibiotic classes is encouraged in this species. This adverse drug effect of fluoroquinolones, and enrofloxacin specifically, has been determined to be species-specific in domestic felids. Four feline-specific missense variants in ABCG2 result in four amino acid changes (E159M, S279L, H283Q, and T644I) that are unique to the domestic cat compared with multiple other nonfeline mammalian species. These changes alter the ABCG2 protein involved with the cellular transmembrane transport of drugs, including fluoroquinolones, making the protein functionally defective in domestic cats. The predisposition to fluoroquinolone-mediated phototoxicity in nondomestic felids was explored in this study. At least eight nondomestic felids share the four ABCG2 missense variants with domestic cats, and eleven other felids shared at least three of the four domestic cat variants. Taken together, these results suggest the genetic potential for nondomestic felids to also experience fluoroquinolone-induced retinal phototoxicity; therefore, cautions similar to those for domestic cats should be followed for these drugs in the entire feline taxon.
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Popp B, Bienvenu T, Giurgea I, Metreau J, Kraus C, Reis A, Fischer J, Bralo MP, Castano JT, Lapunzina P, Almoguera B, Lopez-Grondona F, Sticht H, Zweier C. The recurrent TCF4 missense variant p.(Arg389Cys) causes a neurodevelopmental disorder overlapping with but not typical for Pitt-Hopkins syndrome. Clin Genet 2022; 102:517-523. [PMID: 35908153 PMCID: PMC10108566 DOI: 10.1111/cge.14206] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 11/29/2022]
Abstract
TCF4 haploinsufficiency by deletions, truncating variants or loss-of-function missense variants within the DNA-binding and protein interacting bHLH domain causes Pitt-Hopkins syndrome (PTHS). This neurodevelopmental disorder (NDD) is characterized by severe intellectual disability (ID), epilepsy, hyperbreathing and a typical facial gestalt. Only few aberrations of the N-terminus of TCF4 were associated with milder or atypical phenotypes. By personal communication and searching databases we assembled six cases with the novel, recurrent, de novo missense variant c.1165C > T, p.(Arg389Cys) in TCF4. This variant was identified by diagnostic exome or panel sequencing and is located upstream of the bHLH domain. All six individuals presented with moderate to severe ID with language impairment. Microcephaly occurred in two individuals, epilepsy only in one, and no breathing anomalies or myopia were reported. Facial gestalt showed some aspects of PTHS but was rather non-specific in most individuals. Interestingly, the variant is located within the AD2 activation domain next to a highly conserved coactivator-recruitment motif and might alter interaction with coactivator proteins independently from the bHLH domain. Our findings of a recurrent missense variant outside the bHLH domain in six individuals with an ID phenotype overlapping with but not typical for PTHS delineate a novel genotype-phenotype correlation for TCF4-related NDDs. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Center of Functional Genomics, Berlin, Germany
| | - Thierry Bienvenu
- INSERM U1266, Institut de Psychiatrie et de Neurosciences de Paris, Université de Paris, Paris, France
| | - Irina Giurgea
- Département de Génétique Médicale, INSERM Childhood Genetic Diseases, AP-HP. Sorbonne Université, Hôpital Trousseau, Paris, France
| | - Julia Metreau
- APHP, Service de neurologie pédiatrique, Hôpital Universitaire Bicetre, Le Kremlin-Bicetre, France
| | - Cornelia Kraus
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jan Fischer
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - María Palomares Bralo
- INGEMM, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, IDIPAZ, Madrid, Spain.,ITHACA European Reference Network, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Jair Tenorio Castano
- INGEMM, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, IDIPAZ, Madrid, Spain.,ITHACA European Reference Network, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Pablo Lapunzina
- INGEMM, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, IDIPAZ, Madrid, Spain.,ITHACA European Reference Network, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Berta Almoguera
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Department of Genetics and Genomics, Fundación Jiménez Díaz University Hospital, Madrid, Spain
| | - Fermina Lopez-Grondona
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Department of Genetics and Genomics, Fundación Jiménez Díaz University Hospital, Madrid, Spain
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Christiane Zweier
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
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33
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Varela-Calais P, Nicolicht P, Paulo Martin R, Yamamoto J, D'Almeida V, Maria Martins A, Bosco Pesquero J. Functional characterization of novel variants found in patients with suspected Fabry disease. Clin Chim Acta 2022; 534:156-160. [PMID: 35870541 DOI: 10.1016/j.cca.2022.07.012] [Citation(s) in RCA: 2] [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: 06/01/2022] [Accepted: 07/17/2022] [Indexed: 11/30/2022]
Abstract
The deficiency or absence of the lysosomal hydrolase α-Galactosidase A results in Fabry disease (FD), a rare and underdiagnosed X-linked disorder. The symptoms caused by FD have a direct relation with the variant present in the gene coding α-Galactosidase A (GLA) and enzyme residual activity, and it can vary drastically between men and women of the same family. Here, we present four novel variants found in patients with suspicion of FD. The patients were screened for FD by enzymatic activity and/or DNA sequencing, which showed four novel GLA missense variants. To confirm the potential pathogenicity of these variants, we employed site-directed mutagenesis. GLA wild-type and mutant plasmids were transfected into mammalian cells; RNA and proteins were extracted for expression and enzymatic activity analysis. The patients presented the variants p.Ile133Asn, p.Lys140Thr, p.Lys168Gln and p.Pro323Thr in the GLA. In vitro analysis showed pathogenic potential of three variants and one tolerated variant. The variants p.Ile133Asn and p.Lys168Gln showed no residual activity and, therefore, leading to classical phenotype, and the variant p.Lys140Thr, which presented 22% of residual activity, was considered a mild variant leading to non-classical phenotype. The variant p.Pro323Thr presented 66.7% of residual activity and alone, it is not enough to cause FD.
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Affiliation(s)
- Patrícia Varela-Calais
- Center for Research and Molecular Diagnostic of Genetic Diseases - Department of Biophysics, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Priscila Nicolicht
- Center for Research and Molecular Diagnostic of Genetic Diseases - Department of Biophysics, Federal University of São Paulo, São Paulo, SP, Brazil; Laboratory of Molecular Neurobiology, Universidade Federal de Sao Paulo, Department of Biochemistry, Sao Paulo, Brazil
| | - Renan Paulo Martin
- McKusick-Nathans Department of Genetic Medicine - Johns Hopkins University School of Medicine, Baltimore, MD
| | - Joyce Yamamoto
- Department of Psychobiology, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Vânia D'Almeida
- Department of Psychobiology, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Ana Maria Martins
- Reference Center in Inborn Errors of Metabolism, Pediatrics Department, Federal University of São Paulo, São Paulo, SP, Brazil
| | - João Bosco Pesquero
- Center for Research and Molecular Diagnostic of Genetic Diseases - Department of Biophysics, Federal University of São Paulo, São Paulo, SP, Brazil.
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Meyer AP, Forrest ME, Nicolau S, Wiszniewski W, Bland MP, Tsao CY, Antonellis A, Abreu NJ. Pathogenic missense variants altering codon 336 of GARS1 lead to divergent dominant phenotypes. Hum Mutat 2022; 43:869-876. [PMID: 35332613 PMCID: PMC9247498 DOI: 10.1002/humu.24372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 11/22/2021] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 01/03/2023]
Abstract
Heterozygosity for missense variants and small in-frame deletions in GARS1 has been reported in patients with a range of genetic neuropathies including Charcot-Marie-Tooth disease type 2D (CMT2D), distal hereditary motor neuropathy type V (dHMN-V), and infantile spinal muscular atrophy (iSMA). We identified two unrelated patients who are each heterozygous for a previously unreported missense variant modifying amino-acid position 336 in the catalytic domain of GARS1. One patient was a 20-year-old woman with iSMA, and the second was a 41-year-old man with CMT2D. Functional studies using yeast complementation assays support a loss-of-function effect for both variants; however, this did not reveal variable effects that might explain the phenotypic differences. These cases expand the mutational spectrum of GARS1-related disorders and demonstrate phenotypic variability based on the specific substitution at a single residue.
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Affiliation(s)
- Alayne P. Meyer
- Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Megan E. Forrest
- Department of Human Genetics, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Stefan Nicolau
- The Center for Gene Therapy, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Wojciech Wiszniewski
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, USA
| | - Mary Pat Bland
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, USA
| | - Chang-Yong Tsao
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- Division of Child Neurology, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Neurology, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Anthony Antonellis
- Department of Human Genetics, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
- Department of Neurology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Nicolas J. Abreu
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
- The Center for Gene Therapy, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
- Division of Child Neurology, Nationwide Children's Hospital, Columbus, Ohio, USA
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35
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Waqas A, Nayab A, Shaheen S, Abbas S, Latif M, Rafeeq MM, Al-Dhuayan IS, Alqosaibi AI, Alnamshan MM, Sain ZM, Habib AH, Alam Q, Umair M, Saqib MAN. Case Report: Biallelic Variant in the tRNA Methyltransferase Domain of the AlkB Homolog 8 Causes Syndromic Intellectual Disability. Front Genet 2022; 13:878274. [PMID: 35571055 PMCID: PMC9096442 DOI: 10.3389/fgene.2022.878274] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 02/17/2022] [Accepted: 03/18/2022] [Indexed: 11/23/2022] Open
Abstract
Intellectual disability (ID) has become very common and is an extremely heterogeneous disorder, where the patients face many challenges with deficits in intellectual functioning and adaptive behaviors. A single affected family revealed severe disease phenotypes such as ID, developmental delay, dysmorphic facial features, postaxial polydactyly type B, and speech impairment. DNA of a single affected individual was directly subjected to whole exome sequencing (WES), followed by Sanger sequencing. Data analysis revealed a novel biallelic missense variant (c.1511G>C; p.(Trp504Ser)) in the ALKBH8 gene, which plays a significant role in tRNA modifications. Our finding adds another variant to the growing list of ALKBH8-associated tRNA modifications causing ID and additional phenotypic manifestations. The present study depicts the key role of the genes associated with tRNA modifications, such as ALKBH8, in the development and pathophysiology of the human brain.
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Affiliation(s)
- Ahmed Waqas
- Department of Zoology, Division of Science and Technology, University of Education, Lahore, Pakistan
| | - Anam Nayab
- Microbiology and Biotechnology Research Lab, Department of Biotechnology, Fatima Jinnah Women University, The Mall, Rawalpindi, Pakistan
| | - Shabnam Shaheen
- Department of Higher Education, Government Girls Degree College Lakki Marwat, Lakki Marwat, Pakistan
| | - Safdar Abbas
- Department of Biological Science, Darmouth College, Hanover, NH, United States
| | - Muhammad Latif
- Department of Zoology, Division of Science and Technology, University of Education, Lahore, Pakistan
| | - Misbahuddin M Rafeeq
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abduaziz University, Jeddah, Saudi Arabia
| | - Ibtesam S Al-Dhuayan
- Department of Biology, College of Science, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Amany I Alqosaibi
- Department of Biology, College of Science, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Mashael M Alnamshan
- Department of Biology, College of Science, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Ziaullah M Sain
- Department of Microbiology, Faculty of Medicine, Rabigh, King Abduaziz University, Jeddah, Saudi Arabia
| | - Alaa Hamed Habib
- Department of Physiology, Faculty of Medicine, King Abduaziz University, Jeddah, Saudi Arabia
| | - Qamre Alam
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia.,Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
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36
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Gong L, Wang C, Xie H, Gao J, Li T, Qi S, Wang B, Wang J. Identification of a novel heterozygous SOX9 variant in a Chinese family with congenital heart disease. Mol Genet Genomic Med 2022; 10:e1909. [PMID: 35218327 PMCID: PMC9034670 DOI: 10.1002/mgg3.1909] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/25/2022] [Accepted: 02/14/2022] [Indexed: 12/02/2022] Open
Abstract
Background Previous studies of individuals with hereditary or sporadic congenital heart disease (CHD) have provided strong evidence for a genetic basis for CHD. The aim of this study was to identify novel pathogenic genes and variants in a Chinese CHD family. Methods Three generations of a family with CHD were recruited. We performed whole exome sequencing for the affected individuals and the proband's unaffected aunt to investigate the genetic causes of CHD in this family. Heterozygous variants carried by the proband and her maternal grandmother, but not the proband's aunt, were selected. The frequencies of the variants detected were assessed using public databases, and their influences on protein function were predicted using online prediction software. The candidate variant was further confirmed by Sanger sequencing of other members of the family. Results On the basis of the family's pedigree, the mode of inheritance was speculated to be autosomal dominant with incomplete penetrance. We identified a novel heterozygous missense variant in SOX9 in all affected individuals and one asymptomatic family member, suggesting an inheritance pattern with incomplete penetrance. The variant was not found in any public database. In addition, the variant was highly conserved among mammals, and was predicted to be deleterious by online software programs. Conclusions We report for the first time a novel heterozygous missense variant in SOX9 (NM_000346:c.931G>T:p.Gly311Cys) in a Chinese CHD family. Our results provide further evidence supporting a causative role for SOX9 variants in CHD.
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Affiliation(s)
- Li Gong
- Department of Cardiothoracic Surgery, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Chunyan Wang
- Graduate School of Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China.,Center for Genetics, National Research Institute for Family Planning, Beijing, China
| | - Haiyang Xie
- Department of Cardiothoracic Surgery, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Jun Gao
- Department of Ultrasound imaging, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Tengyan Li
- Center for Genetics, National Research Institute for Family Planning, Beijing, China
| | - Shenggui Qi
- Qinghai High Altitude Medical Research Institute, Xining, China
| | - Binbin Wang
- Graduate School of Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China.,Center for Genetics, National Research Institute for Family Planning, Beijing, China
| | - Jing Wang
- Department of Medical Genetics and Developmental Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China
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Pan X, Liu S, Liu L, Zhang X, Yao H, Tan B. Case Report: Exome and RNA Sequencing Identify a Novel de novo Missense Variant in HNRNPK in a Chinese Patient With Au-Kline Syndrome. Front Genet 2022; 13:853028. [PMID: 35422839 PMCID: PMC9001983 DOI: 10.3389/fgene.2022.853028] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/14/2022] [Indexed: 02/05/2023] Open
Abstract
Au-Kline syndrome is a severe multisystemic syndrome characterized by several congenital defects, including intellectual disability. Loss-of-function and missense variants in the HNRNPK gene are associated with a range of dysmorphic features. This report describes an eleven-year-old Chinese boy with intellectual disability and developmental delays. Family-based whole-exome and Sanger sequencing identified a de novo missense variant in HNRNPK (NM_002140.3: c.143T > A, p. Leu48Val). In silico analysis predicted that this variant would be damaged in a highly conserved residue in the K homology 1 (KH1) domain. Bioinformatic analysis showed that the affinity change (ΔΔG) caused by this variant was -0.033 kcal/mol, indicating that it would have reduced affinity for RNA binding. Transcript analysis of the peripheral blood from this case found 42 aberrantly expressed and 86 aberrantly spliced genes (p-value <0.01). Functional enrichment analysis confirmed that the biological functions of these genes, including protein binding and transcriptional regulation, are associated with HNRNPK. In summary, this study identifies the first Chinese patient with a novel de novo heterozygous HNRNPK gene variant that contributes to Au-Kline syndrome and expands current knowledge of the clinical spectrum of HNRNPK variants.
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Affiliation(s)
- Xin Pan
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Sihan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Li Liu
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xu Zhang
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hong Yao
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Bo Tan
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Zhao X, Zheng Y, Wang L, Wang Y, Mei S, Kong X. A novel variant in UBE3A in a family with multigenerational intellectual disability and developmental delay. Mol Genet Genomic Med 2022; 10:e1883. [PMID: 35225435 PMCID: PMC9000933 DOI: 10.1002/mgg3.1883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 09/09/2021] [Revised: 12/22/2021] [Accepted: 01/14/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Angelman syndrome (AS) is a rare neurodevelopmental disorder and is characterized by severe cognitive disability, motor dysfunction, speech impairment, hyperactivity, and frequent seizures. Although the maternal chromosomal region 15q11.2-q13 deletion is the most common mechanism of AS, ~10% of individuals with AS are caused by the intragenic variants in the maternally inherited UBE3A, which encodes an E3 ubiquitin ligase. METHODS Clinical diagnoses were based on detailed clinical findings. Trio-based exome sequencing was performed on the proband and her parents to identify the underlying genetic variants. The candidate variants were confirmed by Sanger sequencing following PCR amplification. In silico analyses were conducted to predict the effect of the identified variant on the function of UBE3A protein. RESULTS We identified a novel variant c.2029G>C (p. Gly677Arg) in UBE3A as the most promising candidate. In silico analyses showed that p.Gly677Arg in the UBE3A affects a highly conserved residue. Her mother had the variant at this locus. Sanger sequencing results showed that II-2, II-5, II-7, IV-1, III-5, III-7, III-8, and III-9 have the variant c.2029G>C, and all patients inherited maternally variant in UBE3A, while the offsprings of the male carrier were unaffected. CONCLUSIONS We identified a novel variant (c.2029G>C) in the UBE3A in a Chinese family with multigenerational intellectual disability and developmental delay. Our findings expanded the genotypic spectrum of AS and provided important information for genetic counseling.
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Affiliation(s)
- Xuechao Zhao
- Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yuting Zheng
- Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Li Wang
- Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanhong Wang
- Henan Provincial Key Laboratory of Children's Genetics And Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Shiyue Mei
- Henan Provincial Key Laboratory of Children's Genetics And Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Xiangdong Kong
- Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Zhang F, Wang Z, Meng Q, Song J, Yang S, Tang X, Zhao Y, Men S, Wang L. Disparate phenotypes in two unfavorable pregnancies due to maternal mosaicism of a novel RET gene mutation. Clin Chim Acta 2022; 531:84-90. [PMID: 35341763 DOI: 10.1016/j.cca.2022.03.015] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022]
Abstract
Mutations in RET have been found in multiple diseases including isolated and associated congenital anomalies. Here, we report a case presented with disparate phenotypes in each pregnancy but caused by the same novel mutation. Whole-exome sequencing (WES) was performed on the proband/abortion product-parental trio and a novel missense variant in RET (chr10:43615610C>G; c.2689C>G; p.Arg897Gly) was identified. The mother was a low-level somatic carrier of this new mutation, with 17.3% in blood, 19.1% in oralmucous membrane, and 15.7% in urine by droplet digital polymerase chain reaction (dd PCR). Our finding not only broadens the mutation spectrum of RET but also gives supportive genetic counseling and timely guidance on fertility choices.
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Affiliation(s)
- Fang Zhang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Zhiwei Wang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Qian Meng
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Jiedong Song
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Shuting Yang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Xinxin Tang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Yali Zhao
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Shuai Men
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Leilei Wang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China.
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Ullah A, Lin Z, Younus M, Shafiq S, Khan S, Rasheed M, Mahmood A, Alqosaibi AI, Alshehri MA, Khan A, Umair M. Homozygous missense variant in POPDC3 causes recessive limb girdle muscular dystrophy type 26. J Gene Med 2022; 24:e3412. [PMID: 35075722 DOI: 10.1002/jgm.3412] [Citation(s) in RCA: 2] [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: 06/28/2021] [Revised: 10/05/2021] [Accepted: 01/13/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Limb-girdle muscular dystrophy (LGMD) is a heterogeneous group of diseases, which affects different muscles, predominantly skeletal muscles and cardiac muscles of the body. LGMD is classified into two main sub-types A and B, which are further sub-classified into eight dominant and thirty recessive sub-types. Three genes, mainly POPDC1, POPDC2 and POPDC3, encodes popeye domain-containing protein (POPDC), and the variants of POPDC1 and POPDC3 genes have been associated with LGMD. METHODS In this study, we performed whole-exome sequencing (WES) analysis on a single-family to investigate the hallmark features of LGMD. The results of WES were further confirmed by Sanger sequencing and 3D protein modeling was also performed. RESULTS WES data analysis and sanger sequencing revealed a homozygous missense variant (c.460A>G; p.Lys154Glu) at a highly conserved amino acid position in the POPDC3. Mutations in the POPDC3 gene have been previously associated with recessive limb-girdle muscular dystrophy type 26. 3D protein modeling further suggested that the identified variant might affect the POPDC3 structure and proper function. DISCUSSION/CONCLUSIONS This study confirms the role of POPDC3 in LGMD, and will facilitate in genetic counseling of the family to mitigate the risks of the carrier or affected in future pregnancies.
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Affiliation(s)
- Anwar Ullah
- Khyber Medical University Institute of Paramedical Science Peshawar
| | - Zhaohan Lin
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine and Peking-Tsinghua Center for Life Sciences and PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
| | - Muhammad Younus
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine and Peking-Tsinghua Center for Life Sciences and PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
| | - Sarfraz Shafiq
- Department of Anatomy and Cell Biology, Western University, London, ON, Canada
| | - Shazia Khan
- Department of Biological Sciences, International Islamic University Islamabad, H-10, Islamabad, Pakistan
| | - Memoona Rasheed
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, Pakistan
| | - Arif Mahmood
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.,Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Amany I Alqosaibi
- Medical Genetics Laboratory Science, College of Applied medical Sciences, Najran University, Najran, Saudi Arabia
| | - Mohammed Ali Alshehri
- Department of Biology, College of Science, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Amjad Khan
- Faculty of Science, Department of Biological Sciences, University of Lakki Marwat, Pakistan
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia.,Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
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Hegde R, Hegde S, Kulkarni SS, Pandurangi A, Gai PB, Das KK. Genetic analysis of the postsynaptic transmembrane X-linked neuroligin 3 gene in autism. Genomics Inform 2022; 19:e44. [PMID: 35012288 PMCID: PMC8752989 DOI: 10.5808/gi.21029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 04/21/2021] [Accepted: 12/09/2021] [Indexed: 11/20/2022] Open
Abstract
Autism is a complex neurodevelopmental disorder, the prevalence of which has increased drastically in India in recent years. Neuroligin is a type I transmembrane protein that plays a crucial role in synaptogenesis. Alterations in synaptic genes are most commonly implicated in autism and other cognitive disorders. The present study investigated the neuroligin 3 gene in the Indian autistic population by sequencing and in silico pathogenicity prediction of molecular changes. In total, 108 clinically described individuals with autism were included from the North Karnataka region of India, along with 150 age-, sex-, and ethnicity-matched healthy controls. Genomic DNA was extracted from peripheral blood, and exonic regions were sequenced. The functional and structural effects of variants of the neuroligin 3 protein were predicted. One coding sequence variant (a missense variant) and four non-coding variants (two 5'-untranslated region [UTR] variants and two 3'-UTR variants) were recorded. The novel missense variant was found in 25% of the autistic population. The C/C genotype of c.551T>C was significantly more common in autistic children than in controls (p = 0.001), and a significantly increased risk of autism (24.7-fold) was associated with this genotype (p = 0.001). The missense variant showed pathogenic effects and high evolutionary conservation over the functions of the neuroligin 3 protein. In the present study, we reported a novel missense variant, V184A, which causes abnormal neuroligin 3 and was found with high frequency in the Indian autistic population. Therefore, neuroligin is a candidate gene for future molecular investigations and functional analysis in the Indian autistic population.
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Affiliation(s)
- Rajat Hegde
- Laboratory of Vascular Physiology and Medicine, Department of Physiology, Shri B.M Patil Medical College, Hospital and Research Centre, BLDE (Deemed to be University), Vijayapura, Karnataka 586101, India.,Karnataka Institute for DNA Research (KIDNAR), Dharwad, Karnataka 580003, India
| | - Smita Hegde
- Karnataka Institute for DNA Research (KIDNAR), Dharwad, Karnataka 580003, India.,Human Genetics Laboratory, Department. of Anatomy, Shri B.M Patil Medical College, Hospital and Research Centre, BLDE (Deemed to be University), Vijayapura, Karnataka 586101, India
| | | | - Aditya Pandurangi
- Department of Psychiatry, Dharwad Institute of Mental Health and Neurosciences, Dharwad, Karnataka 580008, India
| | - Pramod B Gai
- Karnataka Institute for DNA Research (KIDNAR), Dharwad, Karnataka 580003, India
| | - Kusal K Das
- Laboratory of Vascular Physiology and Medicine, Department of Physiology, Shri B.M Patil Medical College, Hospital and Research Centre, BLDE (Deemed to be University), Vijayapura, Karnataka 586101, India
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Li S, Liu J, Yuan Y, Lu A, Liu F, Sun L, Shen Q, Wang L. Case report: A study on the de novo KMT2D variant of Kabuki syndrome with Goodpasture's syndrome by whole exome sequencing. Front Pediatr 2022; 10:933693. [PMID: 36090579 PMCID: PMC9459111 DOI: 10.3389/fped.2022.933693] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
Kabuki syndrome (KS) is a rare genetic disorder characterized by dysmorphic facial features, skeletal abnormalities, and intellectual disability. KMT2D and KDM6A were identified as the main causative genes. To our knowledge, there exist no cases of KS, which were reported with pneumorrhagia. In this study, a 10-month-old male was diagnosed to have KS with typical facial features, skeletal anomalies, and serious postnatal growth retardation. Whole exome sequencing of the trio family revealed the presence of a de novo KMT2D missense variant (c.15143G > A, p. R5048H). The child was presented to the pediatric emergency department several times because of cough, hypoxemia, and anemia. After performing chest CT and fiberoptic bronchoscopy, we found that the child had a pulmonary hemorrhage. During research on the cause of pulmonary hemorrhage, the patient's anti-GBM antibodies gradually became positive, and the urine microalbumin level was elevated at the age of 12-month-old. After glucocorticoids and immunosuppressant therapy, the patient became much better. But he had recurrent pulmonary hemorrhage at the age of 16 months. Therefore, the patient underwent digital subtraction angiography (DSA). However, the DSA showed three abnormal bronchial arteries. This single case expands the phenotypes of patients with KS and Goodpasture's syndrome, which were found to have a de novo KMT2D missense variant.
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Affiliation(s)
- Shuolin Li
- Department of Respiration, Children's Hospital of Fudan University, Shanghai, China
| | - Jing Liu
- Department of Respiration, Children's Hospital of Fudan University, Shanghai, China
| | - Yuan Yuan
- Department of Respiration, Children's Hospital of Fudan University, Shanghai, China
| | - Aizhen Lu
- Department of Respiration, Children's Hospital of Fudan University, Shanghai, China
| | - Fang Liu
- Department of Cardiovascular, Children's Hospital of Fudan University, Shanghai, China
| | - Li Sun
- Department of Rheumatology, Children's Hospital of Fudan University, Shanghai, China
| | - Quanli Shen
- Department of Radiology, Children's Hospital of Fudan University, Shanghai, China
| | - Libo Wang
- Department of Respiration, Children's Hospital of Fudan University, Shanghai, China
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Asif M, Mocanu ID, Abdullah U, Höhne W, Altmüller J, Makhdoom EUH, Thiele H, Baig SM, Nürnberg P, Graul-Neumann L, Hussain MS. A novel missense variant of SCN4A co-segregates with congenital essential tremor in a consanguineous Kurdish family. Am J Med Genet A 2021; 188:1251-1258. [PMID: 34913263 DOI: 10.1002/ajmg.a.62610] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/10/2021] [Accepted: 11/30/2021] [Indexed: 11/09/2022]
Abstract
Essential tremor (ET) is a neurological disorder characterized by bilateral and symmetric postural, isometric, and kinetic tremors of forelimbs produced during voluntary movements. To date, only a single SCN4A variant has been suggested to cause ET. In continuation of the previous report on the association between SCN4A and ET in a family from Spain, we validated the pathogenicity of a novel SCN4A variant and its involvement in ET in a second family affected by this disease. We recruited a Kurdish family with four affected members manifesting congenital tremor. Using whole-exome sequencing, we identified a novel missense variant in SCN4A, NM_000334.4:c.4679C>T; p.(Pro1560Leu), thus corroborating SCN4A's role in ET. The residue is highly conserved across vertebrates and the substitution is predicted to be pathogenic by various in silico tools. Western blotting and immunocytochemistry performed in cells derived from one of the patients showed reduced immunoreactivity of SCN4A as compared to control cells. The study provides supportive evidence for the role of SCN4A in the etiology of ET and expands the phenotypic spectrum of channelopathies to this neurological disorder.
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Affiliation(s)
- Maria Asif
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Ionut Dragos Mocanu
- Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Uzma Abdullah
- University Institute of Biochemistry and Biotechnology (UIBB), PMAS-Arid Agriculture University, Rawalpindi, Pakistan
| | - Wolfgang Höhne
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Core Facility Genomics, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Ehtisham Ul Haq Makhdoom
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany.,Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE) College, PIEAS, Faisalabad, Pakistan.,Neurochemicalbiology and Genetics Laboratory (NGL), Department of Physiology, Faculty of Life Sciences, Government College University, Faisalabad, Pakistan
| | - Holger Thiele
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Shahid Mahmood Baig
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE) College, PIEAS, Faisalabad, Pakistan.,Pakistan Science Foundation (PSF), Islamabad, Pakistan.,Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Luitgard Graul-Neumann
- Charité-Universitätsmedizin Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany
| | - Muhammad Sajid Hussain
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
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Liang M, Chen C, Dai Y, Chang Y, Gao Y. Two closely spaced missense COL3A1 variants in cis cause vascular Ehlers-Danlos syndrome in one large Chinese family. J Cell Mol Med 2021; 26:144-150. [PMID: 34845833 PMCID: PMC8742230 DOI: 10.1111/jcmm.17063] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 10/10/2021] [Accepted: 10/21/2021] [Indexed: 02/02/2023] Open
Abstract
Vascular Ehlers‐Danlos syndrome (vEDS) is a rare and severe hereditary connective tissue disease arising from a mutation in the type III collagen alpha I chain (COL3A1) gene, with a poor prognosis due to exceptional vascular ruptures and premature death. Herein, starting from a 36‐year‐old Chinese male patient with a complaint of upper abdominal pain, we collected clinical data of and performed a genetic analysis of a total of 20 family members. We identified two closely spaced COL3A1 missense variants in cis, p.Leu734Phe (c.2199_2200TC>AT) and p.Gly741Ser (c.2221G>A), as the cause of vEDS in this family. p.Gly741Ser, a glycine substitution mutation, has been previously reported, whereas p.Leu734Phe, a non‐glycine substitution mutation, is novel. We analysed their independent and combined effects on the COL3A1 level in transfected skin fibroblast cells by means of Western blotting. We found that both variants independently led to a reduced COL3A1 level and, when combined, led to an even more reduced COL3A1 level compared to the wild type. Thus, each missense variant can be independently classified as a pathogenic variant, albeit with a synergetic effect when occurring together. Moreover, our genetic findings provide an explanation for four previous sudden deaths and identified two high‐risk carriers in the family.
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Affiliation(s)
- Mei Liang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chong Chen
- Department of Spine Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yan Dai
- Department of Radiology, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yunbing Chang
- Department of Spine Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yushun Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Umair M, Farooq Khan M, Aldrees M, Nashabat M, Alhamoudi KM, Bilal M, Alyafee Y, Al Tuwaijri A, Aldarwish M, Al-Rumayyan A, Alkhalaf H, Wadaan MAM, Alfadhel M. Mutated VWA8 Is Associated With Developmental Delay, Microcephaly, and Scoliosis and Plays a Novel Role in Early Development and Skeletal Morphogenesis in Zebrafish. Front Cell Dev Biol 2021; 9:736960. [PMID: 34660594 PMCID: PMC8517341 DOI: 10.3389/fcell.2021.736960] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 07/06/2021] [Accepted: 08/26/2021] [Indexed: 11/21/2022] Open
Abstract
Von Willebrand A domain-containing protein 8 (VWA8), also named KIAA0564, is a poorly characterized, mitochondrial matrix-targeted protein having a putative ATPase activity. VWA8 is comprising of ATPase-associated domains and a VWFA domain associated with ATPase activity inside the cell. In the present study, we describe a large consanguineous family of Saudi origin segregating a complex developmental syndrome in an autosomal recessive fashion. All the affected individuals exhibited severe developmental disorders. DNA from three patients was subjected to whole-exome sequencing followed by Sanger sequencing. VWA8 knock-down zebrafish morpholinos were used to study the phenotypic effect of this gene on zebrafish development. A homozygous missense variant [c.947A > G; p.(Asp316Gly)] was identified in exon 8 of the VWA8 gene, which perfectly segregated with the disease phenotype. Using zebrafish morpholino, we observed delayed development at an early stage, lack of movement, light sensitivity, severe skeletal deformity such as scoliosis, and facial dysmorphism. This is the first homozygous variant identified in the VWA8 gene underlying global developmental delay, microcephaly, scoliosis, limbs, and cardiovascular malformations in humans. We provide genetic and molecular evidence using zebrafish morpholino for a homozygous variant in the VWA8 gene, associated with such a complex developmental syndrome in humans.
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Affiliation(s)
- Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Muhammad Farooq Khan
- Bioproducts Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Aldrees
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Marwan Nashabat
- Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children's Hospital, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Kheloud M Alhamoudi
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Muhammad Bilal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Yusra Alyafee
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Abeer Al Tuwaijri
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Manar Aldarwish
- Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children's Hospital, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Ahmed Al-Rumayyan
- Pediatric Neurology Division, Department of Pediatrics, Ministry of National Guard-Health Affairs (MNGHA), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Hamad Alkhalaf
- Department of Pediatrics, Ministry of National Guard-Health Affairs (MNGHA), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Mohammad A M Wadaan
- Bioproducts Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Genetics and Precision Medicine Department (GPM), Ministry of National Guard Health Affairs (MNG-HA), King Abdullah Specialized Children's Hospital (KASCH), King Abdulaziz Medical City, Riyadh, Saudi Arabia
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Saba N, Irshad S. Congenital cataract: An ocular manifestation of classical homocystinuria. Mol Genet Genomic Med 2021; 9:e1742. [PMID: 34342182 PMCID: PMC8457696 DOI: 10.1002/mgg3.1742] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/26/2021] [Accepted: 06/15/2021] [Indexed: 11/23/2022] Open
Abstract
Background Homocystinuria is an autosomal recessive metabolic disorder occurring due to the defects in cystathionine‐β‐synthase enzyme. The study was carried out to investigate a Pakistani family presenting bilateral congenital cataract with symptoms of classical homocystinuria at LRBT Free Eye Hospital, Lahore, Pakistan. Methods Three affected individuals of the family presented skeletal deformations, intellectual disability, speech delay, and myopia with bilateral congenital cataract. Genetic analysis on DNA samples from affected individuals was done through whole exome sequencing to identify underlying genetic variant causing disease phenotypes in the family. In silico analysis was done to predict the effect of variation on the structure of mutant protein. Results A missense allelic variant (NM_000071.3: c.253G>A) of the CBS gene was revealed which may affect the catalytic activity of the substituted (NP_000062.1: p.G85R) protein by disrupting the folding of the enzymatic protein. High levels of homocysteine were observed in the plasma of affected individuals. This is the first report of this genetic variant from Pakistan causing homocystinuria and congenital cataract in association. Conclusion This variant was reported first time in association with congenital cataract instead of ectopia lentis. Congenital cataract was developed secondarily in these patients and provided a clue for the early diagnosis of metabolic disorders like homocystinuria to prevent further complications and morbidity.
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Affiliation(s)
- Neelam Saba
- School of Biochemistry and Biotechnology, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
| | - Saba Irshad
- School of Biochemistry and Biotechnology, University of the Punjab, Quaid-e-Azam Campus, Lahore, Pakistan
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Yu H, He X, Liu X, Zhang H, Shen Z, Shi Y, Liu X. A novel missense variant in cathepsin C gene leads to PLS in a Chinese patient: A case report and literature review. Mol Genet Genomic Med 2021; 9:e1686. [PMID: 33949806 PMCID: PMC8372118 DOI: 10.1002/mgg3.1686] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 03/01/2021] [Accepted: 03/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Papilon-Lefevre syndrome (PLS; OMIM 245000) is a rare autosomal recessive disease characterized by aggressive periodontitis and palmoplantar keratoderma. The prevalence of PLS in the general population is one to four cases per million. Although the etiology and pathogenic mechanisms underlying PLS remain largely unclear, existing evidence shows loss-of-function mutations of the cathepsin C gene (CTSC; OMIM 602365) could cause PLS. Here we found a novel variant of the CTSC gene in a Chinese PLS family and predicted the effect of the variant on the physic-chemical characters and tertiary structure of the protein. METHODS The 1-7 coding exons and exon-intron boundaries of CTSC gene of the proband and her family were amplified and sequenced directly, and Chromas was used to read sequencing files. Furthermore, the PolyPhen-2, PROVEAN, and Mutation Taster were utilized to predict the pathogenicity of the variant. Besides, the physic-chemical and structural characters of the protein were analyzed by ProtParam, ProtScale, and SWISS-MODEL. RESULTS Our study identified a novel homozygous variant c.763T>C (p.Cys255Arg) in exon 6 of the CTSC gene, and it was a likely pathogenic variant as predicted by PolyPhen-2, PROVEAN, and Mutation Taster. Moreover, ProtParam and Protscale revealed the variant increased the isoelectric point and hydrophilicity of the protein, and the SWISS-MODEL analysis suggested the variant was located in a critical domain for protein activity. CONCLUSION Our study analyzed a Chinese family with PLS and identified a novel missense variant in the CTSC gene. Besides, this study retrospectively summarized 113 variants of CTSC in the world and highlighted the features of 27 CTSC variants in Chinese PLS patients. In addition, this study paid much particular attention to the relationship between CTSC variants and different phenotypes.
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Affiliation(s)
- Hui Yu
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China.,Jiangyou People's Hospital, Jiangyou, China
| | - Xun He
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.,Sichuan Provincial Institute of Dermatology and Venereology, Chengdu, China.,Department of Dermatology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Xiangqin Liu
- Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Houbin Zhang
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.,Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China.,Sichuan Provincial Key Laboratory for Human Disease Gene Study, Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Zhu Shen
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.,Sichuan Provincial Institute of Dermatology and Venereology, Chengdu, China.,Department of Dermatology, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Yi Shi
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.,Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China.,Sichuan Provincial Key Laboratory for Human Disease Gene Study, Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Xiaoqi Liu
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.,Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China.,Sichuan Provincial Key Laboratory for Human Disease Gene Study, Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
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Zhang H, Kong X, Ren J, Yuan S, Liu C, Hou Y, Liu Y, Meng L, Zhang G, Du Q, Shen W. A novel EDAR missense mutation identified by whole-exome sequencing with non-syndromic tooth agenesis in a Chinese family. Mol Genet Genomic Med 2021; 9:e1684. [PMID: 33943035 PMCID: PMC8222839 DOI: 10.1002/mgg3.1684] [Citation(s) in RCA: 7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 02/06/2023] Open
Abstract
Background Causative variants in genes of the EDA/EDAR/NF‐κB pathway, such as EDA and EDARADD, have been widely identified in patients with non‐syndromic tooth agenesis (NSTA). However, few cases of NSTA are due to ectodysplasin‐A receptor (EDAR) variants. In this study, we investigated NSTA‐associated variants in Chinese families. Methods Peripheral blood samples were collected from the family members of 24 individuals with NSTA for DNA extraction. The coding region of the EDA gene of the 24 probands was amplified by PCR and sequenced to investigate new variants. Whole‐exome sequencing and Sanger sequencing were then performed for probands without EDA variants detected by PCR. Results A novel missense variant EDAR c.338G>A (p.(Cys113Tyr)) was identified in one family. In addition, three known EDA variants (c.865C>T, c.866G>A, and c.1013C>T) were identified in three families. Genotype–phenotype correlation analysis of EDAR gene mutation showed that NSTA patients were most likely to lose the maxillary lateral incisors and the maxillary central incisors were the least affected. The phenotype of mutations at codon 289 of EDA in NSTA affected patients was characterized by lateral incisors loss, rarely affecting the maxillary first molars. Conclusion A novel EDAR missense variant c.338G>A (p.(Cys113Tyr)) was identified in a family with NSTA, extending the mutation spectrum of the EDAR gene. Genotype–phenotype correlation analyses of EDAR and EDA mutations could help to improve disease status prediction in NSTA families.
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Affiliation(s)
- Hongyu Zhang
- Department of Prosthodontics, Hebei Key Laboratory of Stomatology, Hebei Clinical Research Center for Oral Diseases, School and Hospital of Stomatology, Hebei Medical University, Shijiazhuang, PR China
| | - Xuanting Kong
- Department of Prosthodontics, Hebei Key Laboratory of Stomatology, Hebei Clinical Research Center for Oral Diseases, School and Hospital of Stomatology, Hebei Medical University, Shijiazhuang, PR China
| | - Jiabao Ren
- Department of Prosthodontics, Hebei Key Laboratory of Stomatology, Hebei Clinical Research Center for Oral Diseases, School and Hospital of Stomatology, Hebei Medical University, Shijiazhuang, PR China
| | - Shuo Yuan
- Department of Prosthodontics, Hebei Key Laboratory of Stomatology, Hebei Clinical Research Center for Oral Diseases, School and Hospital of Stomatology, Hebei Medical University, Shijiazhuang, PR China
| | - Chunyan Liu
- Department of Orthodontics, Hebei Key Laboratory of Stomatology, Hebei Clinical Research Center for Oral Diseases, School and Hospital of Stomatology, Hebei Medical University, Shijiazhuang, PR China
| | - Yan Hou
- Department of Orthodontics, Hebei Key Laboratory of Stomatology, Hebei Clinical Research Center for Oral Diseases, School and Hospital of Stomatology, Hebei Medical University, Shijiazhuang, PR China
| | - Ye Liu
- Department of Orthodontics, Hebei Key Laboratory of Stomatology, Hebei Clinical Research Center for Oral Diseases, School and Hospital of Stomatology, Hebei Medical University, Shijiazhuang, PR China
| | - Lingqiang Meng
- Department of Prosthodontics, Hebei Key Laboratory of Stomatology, Hebei Clinical Research Center for Oral Diseases, School and Hospital of Stomatology, Hebei Medical University, Shijiazhuang, PR China
| | - Guozhong Zhang
- College of Forensic Medicine, Hebei Medical University, Shijiazhuang, PR China
| | - Qingqing Du
- College of Forensic Medicine, Hebei Medical University, Shijiazhuang, PR China
| | - Wenjing Shen
- Department of Prosthodontics, Hebei Key Laboratory of Stomatology, Hebei Clinical Research Center for Oral Diseases, School and Hospital of Stomatology, Hebei Medical University, Shijiazhuang, PR China
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Xiaozhen S, Fan Y, Fang Y, Xiaoping L, Jia J, Wuhen X, Xiaojun T, Jun S, Yucai C, Hong Z, Guang H, Shengnan W. Novel Truncating and Missense Variants in SEMA6B in Patients With Early-Onset Epilepsy. Front Cell Dev Biol 2021; 9:633819. [PMID: 34017830 PMCID: PMC8129541 DOI: 10.3389/fcell.2021.633819] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 11/26/2020] [Accepted: 03/17/2021] [Indexed: 11/13/2022] Open
Abstract
Progressive myoclonic epilepsy (PME) is a rare neurodegenerative disease, characterized by myoclonic seizures and tonic clonic seizures, with genetical and phenotypical heterogeneity. The semaphorin 6B (SEMA6B) gene has been recently reported a causal gene of PME. Independent studies are warranted to further support these findings. Here we report that one nonsense variant in NM_032108.3 exon17 c.2056C > T (p.Gln686∗) and one missense variant in exon14 c.1483G > T (p.Gly495Trp) of SEMA6B, both occurring de novo, underlie early-onset epilepsy with variable severity and different response to treatment in two patients. In vitro analyses have demonstrated that the nonsense variant, p.Gln686∗, results in a truncated protein with remarkably increased expression compared to that of the wild type. The truncated protein presented more homogeneous and failed to locate in the plasma membrane. The missense variant p.Gly495Trp affects evolutionarily conserved amino acid and is located in the sema domain, a key functional domain of SEMA6B. It was predicted to perturb the SEMA6B function by altering the tertiary structure of mutant protein, although neither change of protein length and expression nor difference of cellular distribution was observed. Co-immunoprecipitation studies have demonstrated that both variants influence protein binding of SEMA6B and PlxnA2 with varying degrees. Our results provide further evidence to support the initial findings of SEMA6B being causal to epilepsy and indicate that mediating Semaphorin/Plexin signaling is the potential mechanism of the SEMA6B-related disease.
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Affiliation(s)
- Song Xiaozhen
- Laboratory of Molecular Diagnosis, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yuan Fan
- Bio-X Institute, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Psychotic Disorders, Shanghai Institute of Mental Health, Shanghai Jiao Tong University, Shanghai, China
| | - Yuan Fang
- Department of Neurology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Lan Xiaoping
- Laboratory of Molecular Diagnosis, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jia Jia
- Fuxiang Gene Engineering Research Institute, Shanghai, China
| | - Xu Wuhen
- Laboratory of Molecular Diagnosis, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Tang Xiaojun
- Laboratory of Molecular Diagnosis, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Shen Jun
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Chen Yucai
- Department of Neurology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhang Hong
- Laboratory of Molecular Diagnosis, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - He Guang
- Bio-X Institute, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Psychotic Disorders, Shanghai Institute of Mental Health, Shanghai Jiao Tong University, Shanghai, China
| | - Wu Shengnan
- Laboratory of Molecular Diagnosis, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
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Fatima A, Hoeber J, Schuster J, Koshimizu E, Maya-Gonzalez C, Keren B, Mignot C, Akram T, Ali Z, Miyatake S, Tanigawa J, Koike T, Kato M, Murakami Y, Abdullah U, Ali MA, Fadoul R, Laan L, Castillejo-López C, Liik M, Jin Z, Birnir B, Matsumoto N, Baig SM, Klar J, Dahl N. Monoallelic and bi-allelic variants in NCDN cause neurodevelopmental delay, intellectual disability, and epilepsy. Am J Hum Genet 2021; 108:739-748. [PMID: 33711248 PMCID: PMC8059333 DOI: 10.1016/j.ajhg.2021.02.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/21/2021] [Indexed: 12/14/2022] Open
Abstract
Neurochondrin (NCDN) is a cytoplasmatic neural protein of importance for neural growth, glutamate receptor (mGluR) signaling, and synaptic plasticity. Conditional loss of Ncdn in mice neural tissue causes depressive-like behaviors, impaired spatial learning, and epileptic seizures. We report on NCDN missense variants in six affected individuals with variable degrees of developmental delay, intellectual disability (ID), and seizures. Three siblings were found homozygous for a NCDN missense variant, whereas another three unrelated individuals carried different de novo missense variants in NCDN. We assayed the missense variants for their capability to rescue impaired neurite formation in human neuroblastoma (SH-SY5Y) cells depleted of NCDN. Overexpression of wild-type NCDN rescued the neurite-phenotype in contrast to expression of NCDN containing the variants of affected individuals. Two missense variants, associated with severe neurodevelopmental features and epilepsy, were unable to restore mGluR5-induced ERK phosphorylation. Electrophysiological analysis of SH-SY5Y cells depleted of NCDN exhibited altered membrane potential and impaired action potentials at repolarization, suggesting NCDN to be required for normal biophysical properties. Using available transcriptome data from human fetal cortex, we show that NCDN is highly expressed in maturing excitatory neurons. In combination, our data provide evidence that bi-allelic and de novo variants in NCDN cause a clinically variable form of neurodevelopmental delay and epilepsy, highlighting a critical role for NCDN in human brain development.
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