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Wang L, Xu H, Shu J, Yan D, Li D, Cai C. Case Report: A developmental and epileptic encephalopathy 45 due to de novo variant of GABRB1. Front Pediatr 2024; 12:1346987. [PMID: 38633326 PMCID: PMC11021647 DOI: 10.3389/fped.2024.1346987] [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: 11/30/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
Background The gamma-aminobutyric acid (GABA) variant causes developmental and epileptic encephalopathy 45 (DEE45), an autosomal dominant disorder that results in oculocortical visual impairment, reduced muscle tone, psychomotor retardation, and epilepsy. Analysis of the clinical features and genetics of DEE45 may be helpful in complementing genotype-phenotype studies. Case presentation We collected peripheral blood samples from the affected children and parents and extracted genomic DNA. Whole exome sequencing (WES) was utilized to identify the underlying disease-causing variant. WES showed that the prior carried a heterozygous variant c.686C > T p.(Ala229Val) in exon 7 of the GABRB1 (NM_000812.4), and no variant was detected in either parental sample. The child has DEE45. Conclusion The variant c.686C > T of the GABRB1 is a possible cause of DEE45. Gene variant analysis of the relevant family lines using WES provides effective genetic counseling for developing and regressing such patients in the clinic. However, further studies are needed to verify the pathogenic mechanism.
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Affiliation(s)
- Lu Wang
- Tianjin Pediatric Research Institute, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Haiquan Xu
- Department of Neurology, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China
| | - Jianbo Shu
- Tianjin Pediatric Research Institute, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Dandan Yan
- Tianjin Pediatric Research Institute, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Dong Li
- Department of Neurology, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China
| | - Chunquan Cai
- Tianjin Pediatric Research Institute, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
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2
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Nakamura T, Ueda J, Mizuno S, Honda K, Kazuno AA, Yamamoto H, Hara T, Takata A. Topologically associating domains define the impact of de novo promoter variants on autism spectrum disorder risk. Cell Genom 2024; 4:100488. [PMID: 38280381 PMCID: PMC10879036 DOI: 10.1016/j.xgen.2024.100488] [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: 04/14/2023] [Revised: 08/24/2023] [Accepted: 01/02/2024] [Indexed: 01/29/2024]
Abstract
Whole-genome sequencing (WGS) studies of autism spectrum disorder (ASD) have demonstrated the roles of rare promoter de novo variants (DNVs). However, most promoter DNVs in ASD are not located immediately upstream of known ASD genes. In this study analyzing WGS data of 5,044 ASD probands, 4,095 unaffected siblings, and their parents, we show that promoter DNVs within topologically associating domains (TADs) containing ASD genes are significantly and specifically associated with ASD. An analysis considering TADs as functional units identified specific TADs enriched for promoter DNVs in ASD and indicated that common variants in these regions also confer ASD heritability. Experimental validation using human induced pluripotent stem cells (iPSCs) showed that likely deleterious promoter DNVs in ASD can influence multiple genes within the same TAD, resulting in overall dysregulation of ASD-associated genes. These results highlight the importance of TADs and gene-regulatory mechanisms in better understanding the genetic architecture of ASD.
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Affiliation(s)
- Takumi Nakamura
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Junko Ueda
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Shota Mizuno
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kurara Honda
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - An-A Kazuno
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hirona Yamamoto
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Tomonori Hara
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Organ Anatomy, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Atsushi Takata
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan.
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Chen M, Shen MC, Chang SP, Ma GC, Lee DJ, Yan A. De Novo Noninversion Variants Implicated in Sporadic Hemophilia A: A Variant Origin and Timing Study. Int J Mol Sci 2024; 25:1763. [PMID: 38339041 PMCID: PMC10855912 DOI: 10.3390/ijms25031763] [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: 11/15/2023] [Revised: 01/26/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
Sporadic hemophilia A (HA) enables the persistence of HA in the population. F8 gene inversion originates mainly in male germ cells during meiosis. To date, no studies have shown the origin and timing of HA sporadic noninversion variants (NIVs); herein, we assume that HA-sporadic NIVs are generated as a de novo variant. Of the 125 registered families with HA, 22 were eligible for inclusion. We conducted a linkage analysis using F8 gene markers and amplification refractory mutation system-quantitative polymerase chain reaction to confirm the origin of the sporadic NIVs (~0% mutant cells) or the presence of a mosaic variant, which requires further confirmation of the origin in the parent. Nine mothers, four maternal grandmothers, and six maternal grandfathers were confirmed to be the origin of sporadic NIVs, which most likely occurred in the zygote within the first few cell divisions and in single sperm cells, respectively. Three mothers had mosaic variants, which most likely occurred early in postzygotic embryogenesis. All maternal grandparents were free from sporadic NIV. In conclusion, F8 NIVs in sporadic HA were found to be caused primarily by de novo variants. Our studies are essential for understanding the genetic pathogenesis of HA and improving current genetic counseling.
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Affiliation(s)
- Ming Chen
- Department of Genomic Medicine, Changhua Christian Hospital, Changhua 500, Taiwan; (M.C.); (S.-P.C.); (G.-C.M.); (D.-J.L.); (A.Y.)
- Department of Obstetrics and Gynecology, Changhua Christian Hospital, Changhua 500, Taiwan
- Department of Medical Genetics National Taiwan University Hospital, Taipei 100, Taiwan
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Ming-Ching Shen
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei 100, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan
- Hemophilia Treatment and Thrombosis Center, Department of Internal Medicine, Changhua Christian Hospital, Changhua 500, Taiwan
| | - Shun-Ping Chang
- Department of Genomic Medicine, Changhua Christian Hospital, Changhua 500, Taiwan; (M.C.); (S.-P.C.); (G.-C.M.); (D.-J.L.); (A.Y.)
| | - Gwo-Chin Ma
- Department of Genomic Medicine, Changhua Christian Hospital, Changhua 500, Taiwan; (M.C.); (S.-P.C.); (G.-C.M.); (D.-J.L.); (A.Y.)
| | - Dong-Jay Lee
- Department of Genomic Medicine, Changhua Christian Hospital, Changhua 500, Taiwan; (M.C.); (S.-P.C.); (G.-C.M.); (D.-J.L.); (A.Y.)
| | - Adeline Yan
- Department of Genomic Medicine, Changhua Christian Hospital, Changhua 500, Taiwan; (M.C.); (S.-P.C.); (G.-C.M.); (D.-J.L.); (A.Y.)
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Zhang Q, Liu Y, Liu X, Zhao Y, Zhang J. A novel CTBP1 variant in a Chinese pediatric patient with a phenotype distinct from hypotonia, ataxia, developmental delay, and tooth enamel defect syndrome. Front Genet 2024; 15:1344682. [PMID: 38348454 PMCID: PMC10859494 DOI: 10.3389/fgene.2024.1344682] [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: 11/26/2023] [Accepted: 01/10/2024] [Indexed: 02/15/2024] Open
Abstract
Hypotonia, Ataxia, Developmental Delay, and Tooth Enamel Defect Syndrome (HADDTS) is an exceptionally rare disorder resulting from a heterozygous variant in the C-terminal binding protein 1 (CTBP1) gene. To date, a mere two variants (14 patients) have been documented on a global scale. The aim of this study was to identify a causative CTBP1 variant in a Chinese patient, and to determine the potential pathogenicity of the identified variant. Here, Whole-exome sequencing (WES) was conducted on the proband to pinpoint the candidate variant. Following this, Sanger sequencing was employed to validate the identified candidate variant and examine its co-segregation within the available family members. Employing both in silico prediction and three-dimensional protein modeling, we conducted an analysis to assess the potential functional implications of the variant on the encoded protein. Our investigation led to the identification of a novel heterozygous variant in the CTBP1 gene, namely, c.371 C>T (p.Ser124Phe), in a Chinese patient. This case represents the first confirmed instance of such a variant in a Chinese patient. When comparing the patient's clinical symptoms with those reported in the literature, notable distinctions were observed between her primary symptoms and those associated with HADDTS. She showed other signs such as microcephaly, coarse facial features, single transverse palmar crease, visible beard, myopia, coarse toenail and skeletal anomalies. This study enriching the spectrum of genetic variants observed in different ethnic populations and expanding the phenotypic profile associated with this gene. These findings are expected to contribute to the enhancement of future variant-based screening and genetic diagnosis, while also providing further insights into the pathogenic mechanisms underlying CTBP1-related conditions.
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Affiliation(s)
- Qiang Zhang
- Hematology Laboratory, Sheng Jing Hospital of China Medical University, Shenyang, China
- The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Guangxi Birth Defects Prevention and Control Institute, Nanning, China
| | - Yusi Liu
- Hematology Laboratory, Sheng Jing Hospital of China Medical University, Shenyang, China
| | - Xuan Liu
- Hematology Laboratory, Sheng Jing Hospital of China Medical University, Shenyang, China
| | - Yue Zhao
- Hematology Laboratory, Sheng Jing Hospital of China Medical University, Shenyang, China
| | - Jihong Zhang
- Hematology Laboratory, Sheng Jing Hospital of China Medical University, Shenyang, China
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Yi S, Tang X, Chen F, Wang L, Chen J, Yang Z, Huang M, Yi S, Huang L, Yang Q, Yang S, Pan P, Qin Z, Luo J. A genetic variant in the MAST1 gene is associated with mega-corpus-callosum syndrome with hypoplastic cerebellar vermis, in a fetus. Mol Genet Genomic Med 2024; 12:e2358. [PMID: 38284444 PMCID: PMC10785557 DOI: 10.1002/mgg3.2358] [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: 06/27/2023] [Revised: 12/14/2023] [Accepted: 12/26/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Mega-corpus-callosum syndrome with cerebellar hypoplasia and cortical malformations is a rare neurological disorder that is associated with typical clinical and imaging features. The syndrome is caused by pathogenic variants in the MAST1 gene, which encodes a microtubule-associated protein that is predominantly expressed in postmitotic neurons in the developing nervous system. METHODS Fetal DNA from umbilical cord blood samples and genomic DNA from peripheral blood lymphocytes were subjected to whole-exome sequencing. The potential causative variants were verified by Sanger sequencing. RESULTS A 26-year-old primigravid woman was referred to our prenatal center at 25 weeks of gestation due to abnormal ultrasound findings in the brain of the fetus. The brain abnormalities included wide cavum septum pellucidum, shallow and incomplete bilateral lateral fissure cistern, bilateral dilated lateral ventricles, hyperplastic corpus callosum, lissencephaly, and cortical dysplasia. No obvious abnormalities were observed in the brainstem or cerebellum hemispheres, but the cerebellum vermis was small. Whole-exome sequencing identified a de novo, heterozygous missense variant, c.695T>C(p.Leu232Pro), in the MAST1 gene and a genetic diagnosis of mega-corpus-callosum syndrome was considered. CONCLUSION This study is the first prenatal case of MAST1-related disorder reported in the Chinese population and has expanded the mutation spectrum of the MAST1 gene.
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Affiliation(s)
- Sheng Yi
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention InstituteMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and PreventionMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Xianglian Tang
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention InstituteMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and PreventionMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Fei Chen
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention InstituteMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and PreventionMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Linlin Wang
- Department of ObstetricsMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Junjie Chen
- Department of RadiologyMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Zuojian Yang
- Department of UltrasoundMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Minpan Huang
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention InstituteMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and PreventionMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Shang Yi
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention InstituteMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and PreventionMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Limei Huang
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention InstituteMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and PreventionMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Qi Yang
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention InstituteMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and PreventionMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Shuihua Yang
- Department of UltrasoundMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Pingshan Pan
- Department of ObstetricsMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Zailong Qin
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention InstituteMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and PreventionMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
| | - Jingsi Luo
- Genetic and Metabolic Central Laboratory, Guangxi Birth Defects Research and Prevention InstituteMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
- Guangxi Clinical Research Center for Pediatric Diseases, Guangxi Key Laboratory of Reproductive Health and Birth Defects Prevention, Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Guangxi Key Laboratory of Birth Defects and Stem Cell Biobank, Guangxi Key Laboratory of Birth Defects Research and PreventionMaternal and Child Health Hospital of Guangxi Zhuang Autonomous RegionNanningChina
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Togashi T, Nagaya S, Meguro-Horike M, Matsumoto H, Imai Y, Yamaguchi K, Fujii Y, Moriya H, Kikuchi Y, Yasuda I, Horike SI, Morishita E. Identification of two de novo variants causing inherited antithrombin deficiency by quantitative analysis of variant alleles. Thromb Res 2024; 233:37-40. [PMID: 37995440 DOI: 10.1016/j.thromres.2023.11.016] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/04/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Affiliation(s)
- Tomoki Togashi
- Department of Clinical Laboratory Science, Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa 920-0942, Japan
| | - Satomi Nagaya
- Department of Clinical Laboratory Science, Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa 920-0942, Japan
| | - Makiko Meguro-Horike
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Haruto Matsumoto
- Department of Clinical Laboratory Science, Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa 920-0942, Japan
| | - Yuta Imai
- Department of Clinical Laboratory Science, Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa 920-0942, Japan
| | - Koichi Yamaguchi
- Department of Clinical Laboratory Science, Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa 920-0942, Japan; Department of Medical Technology, Faculty of Health Science, Tsukuba International University, 6-20-1 Tsuchiura, Ibaraki 300-0051, Japan
| | - Yoshinari Fujii
- Department of Clinical Laboratory Science, Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa 920-0942, Japan; Department of Medical Technology and Clinical Engineering, Faculty of Health and Medical Sciences, Hokuriku University, 1-1 Taiyogaoka, Kanazawa, Ishikawa 920-1180, Japan
| | - Haruka Moriya
- Department of Clinical Laboratory Science, Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa 920-0942, Japan
| | - Yuika Kikuchi
- Department of Clinical Laboratory Science, Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa 920-0942, Japan
| | - Ibuki Yasuda
- Department of Clinical Laboratory Science, Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa 920-0942, Japan
| | - Shin-Ichi Horike
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Eriko Morishita
- Department of Clinical Laboratory Science, Division of Health Sciences, Graduate School of Medical Science, Kanazawa University, 5-11-80 Kodatsuno, Kanazawa, Ishikawa 920-0942, Japan; Department of Hematology, Kanazawa University Hospital, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8640, Japan.
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Zhao W, Zhang Y, Lv T, He J, Zhu B. A case report of a novel HIST1H1E mutation and a review of the bibliography to evaluate the genotype-phenotype correlations. Mol Genet Genomic Med 2023; 11:e2273. [PMID: 37605493 PMCID: PMC10724515 DOI: 10.1002/mgg3.2273] [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: 01/19/2023] [Revised: 04/14/2023] [Accepted: 08/08/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND HIST1H1E is a member of the H1 gene family. Excess de novo likely gene-disruptive variants involving the C-terminal tail of HIST1H1E have been reported in neurodevelopmental disorders. Although clinical phenotypes in some patients have been described in single studies, few studies have reviewed the genotype and phenotype relationships using a relatively large cohort of patients with HIST1H1E variants. METHODS Whole-exome sequencing (WES) was performed on the proband. The variant was validated using Sanger sequencing in both proband and parents. Published HIST1H1E variants in neuropsychiatric disorders were reviewed. RESULTS Herein, we reported a new de novo frameshift mutation in HIST1H1E (NM_005321.2, c.416_419dupAGAA, p.Ala141GlufsTer56) in an individual with Rahman syndrome. To explore the genotype-phenotype correlations for HIST1H1E variants in neurodevelopmental disorders, we comprehensively curated and summarized 23 variants and the clinical features from 52 patients. Our findings revealed that likely gene-disrupting variants in HIST1H1E contribute to a wide range of neurodevelopmental phenotypes. We observed the common phenotypes including craniofacial features, ID, hypotonia, and autism/behavior problem in patients with HIST1H1E variants. While the different genotypes corresponding to different phenotypes or the same phenotype were also observed. CONCLUSION These data provide scientific evidence for the genetic diagnosis and precision clinical management.
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Affiliation(s)
- Wenjing Zhao
- Department of Medical Genetics, First People's Hospital of Yunnan ProvinceKunmingChina
- Affiliated Hospital of Kunming University of Science and TechnologyKunmingChina
- National Health CommissionKey Laboratory of Preconception Health Birth in Western ChinaKunmingChina
| | - Yinhong Zhang
- Department of Medical Genetics, First People's Hospital of Yunnan ProvinceKunmingChina
- Affiliated Hospital of Kunming University of Science and TechnologyKunmingChina
- National Health CommissionKey Laboratory of Preconception Health Birth in Western ChinaKunmingChina
| | - Tao Lv
- Department of Medical Genetics, First People's Hospital of Yunnan ProvinceKunmingChina
- Affiliated Hospital of Kunming University of Science and TechnologyKunmingChina
- National Health CommissionKey Laboratory of Preconception Health Birth in Western ChinaKunmingChina
| | - Jing He
- Department of Medical Genetics, First People's Hospital of Yunnan ProvinceKunmingChina
- Affiliated Hospital of Kunming University of Science and TechnologyKunmingChina
- National Health CommissionKey Laboratory of Preconception Health Birth in Western ChinaKunmingChina
| | - Baosheng Zhu
- Department of Medical Genetics, First People's Hospital of Yunnan ProvinceKunmingChina
- Affiliated Hospital of Kunming University of Science and TechnologyKunmingChina
- National Health CommissionKey Laboratory of Preconception Health Birth in Western ChinaKunmingChina
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Erratum: A self-repair history: compensatory effect of a de novo variant on the FANCA c.2778+83C>G splicing mutation. Front Genet 2023; 14:1293778. [PMID: 37799138 PMCID: PMC10548262 DOI: 10.3389/fgene.2023.1293778] [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: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 10/07/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fgene.2023.1209138.].
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9
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Janssens V, Wadzinski BE, Li C, Honkanen RE. Editorial: Deciphering the etiology of rare genetic disorders associated with protein phosphatases. Front Cell Dev Biol 2023; 11:1241606. [PMID: 37645249 PMCID: PMC10461562 DOI: 10.3389/fcell.2023.1241606] [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: 06/16/2023] [Accepted: 07/31/2023] [Indexed: 08/31/2023] Open
Affiliation(s)
- Veerle Janssens
- Laboratory of Protein Phosphorylation and Proteomics, Department of Cellular and Molecular Medicine, University of Leuven (KU Leuven), Leuven, Belgium
- KU Leuven Brain Institute (LBI), Leuven, Belgium
- KU Leuven Cancer Institute (LKI), Leuven, Belgium
| | - Brian E. Wadzinski
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Chenchen Li
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL, United States
| | - Richard E. Honkanen
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL, United States
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10
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Persico I, Fontana G, Faleschini M, Zanchetta ME, Ammeti D, Cappelli E, Corsolini F, Mosa C, Guarina A, Bogliolo M, Surrallés J, Dufour C, Farruggia P, Savoia A, Bottega R. A self-repair history: compensatory effect of a de novo variant on the FANCA c.2778+83C>G splicing mutation. Front Genet 2023; 14:1209138. [PMID: 37547463 PMCID: PMC10397729 DOI: 10.3389/fgene.2023.1209138] [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: 04/20/2023] [Accepted: 07/05/2023] [Indexed: 08/08/2023] Open
Abstract
Introduction: Fanconi anemia (FA) is a genome instability condition that drives somatic mosaicism in up to 25% of all patients, a phenomenon now acknowledged as a good prognostic factor. Herein, we describe the case of P1, a FA proband carrying a splicing variant, molecularly compensated by a de novo insertion. Methods and Results: Targeted next-generation sequencing on P1's peripheral blood DNA detected the known FANCA c.2778 + 83C > G intronic mutation and suggested the presence of a large deletion on the other allele, which was then assessed by MLPA and RT-PCR. To determine the c.2778 + 83C > G splicing effect, we performed a RT-PCR on P1's lymphoblastoid cell line (LCL) and on the LCL of another patient (P2) carrying the same variant. Although we confirmed the expected alternative spliced form with a partial intronic retention in P2, we detected no aberrant products in P1's sample. Sequencing of P1's LCL DNA allowed identification of the de novo c.2778 + 86insT variant, predicted to compensate 2778 + 83C > G impact. Albeit not found in P1's bone marrow (BM) DNA, c.2778 + 86insT was detected in a second P1's LCL established afterward, suggesting its occurrence at a low level in vivo. Minigene assay recapitulated the c.2778 + 83C > G effect on splicing and the compensatory role of c.2778 + 86insT in re-establishing the physiological mechanism. Accordingly, P1's LCL under mitomycin C selection preserved the FA pathway activity in terms of FANCD2 monoubiquitination and cell survival. Discussion: Our findings prove the role of c.2778 + 86insT as a second-site variant capable of rescuing c.2778 + 83C > G pathogenicity in vitro, which might contribute to a slow hematopoietic deterioration and a mild hematologic evolution.
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Affiliation(s)
- Ilaria Persico
- Department of Medical Sciences, University of Trieste, Trieste, Italy
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
- Genomic Instability DNA Repair Syndromes Group, Joint Research Unit in Genomic Medicine UAB-IR Sant Pau, Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona, Spain
| | - Giorgia Fontana
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, Trieste, Italy
| | - Michela Faleschini
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, Trieste, Italy
| | | | - Daniele Ammeti
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, Trieste, Italy
| | - Enrico Cappelli
- Hematology Unit, IRCCS Istituto “G. Gaslini”—Genoa, Genova, Italy
| | - Fabio Corsolini
- LABSIEM—Laboratory for the Study of Inborn Errors of Metabolism—Pediatric Clinic and Endocrinology—IRCCS Istituto “G. Gaslini”—Genoa, Genova, Italy
| | - Clara Mosa
- Pediatric Onco-Hematology, ARNAS Civico Hospital, Palermo, Italy
| | - Angela Guarina
- Pediatric Onco-Hematology, ARNAS Civico Hospital, Palermo, Italy
| | - Massimo Bogliolo
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
- Genomic Instability DNA Repair Syndromes Group, Joint Research Unit in Genomic Medicine UAB-IR Sant Pau, Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona, Spain
| | - Jordi Surrallés
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
- Genomic Instability DNA Repair Syndromes Group, Joint Research Unit in Genomic Medicine UAB-IR Sant Pau, Sant Pau Biomedical Research Institute (IIB Sant Pau), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Carlos III Health Institute, Madrid, Spain
| | - Carlo Dufour
- Hematology Unit, IRCCS Istituto “G. Gaslini”—Genoa, Genova, Italy
| | - Piero Farruggia
- Pediatric Onco-Hematology, ARNAS Civico Hospital, Palermo, Italy
| | - Anna Savoia
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Roberta Bottega
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, Trieste, Italy
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11
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Trieschmann G, Wilhelm C, Berweck S, Zech M. De novo retinoic acid receptor beta (RARB) variant associated with microphthalmia and dystonia. Eur J Med Genet 2023; 66:104802. [PMID: 37321544 DOI: 10.1016/j.ejmg.2023.104802] [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: 04/03/2023] [Revised: 05/30/2023] [Accepted: 06/12/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Definition of the individual genotypes that cause a Mendelian phenotype is of great importance both to clinical diagnostics and disease characterization. Heterozygous de novo gain-of-function missense variants in RARB are associated with syndromic microphthalmia 12 (MCOPS12), a developmental disorder characterized by eye malformations and variable involvement of other organs. A subset of patients were described with poorly delineated movement disorders. Additionally, RARB bi-allelic loss-of-function variants, inherited from asymptomatic heterozygous carrier parents, have been found in a recessive family with four MCOPS12-affected members. PATIENT/METHODS We used trio whole-exome sequencing to explore the molecular basis of disease in an individual with congenital eye abnormality and movement disorder. All patients with reported RARB variants were reviewed. RESULTS We report on identification of a heterozygous de novo RARB nonsense variant in a girl with microphthalmia and progressive generalized dystonia. Public database entries indicate that the de novo variant is recurrently present in clinically affected subjects but a literature report has not yet been available. CONCLUSIONS We provide the first detailed evidence for a role of dominant RARB truncating alterations in congenital eye-brain disease, expanding the spectrum of MCOPS12-associated mutations. Considered together with the published family with bi-allelic variants, the data suggest manifestation and non-manifestation of disease in relation to almost identical RARB loss-of-function variations, an apparent paradox that is seen in a growing number of human genetic conditions associated with both recessive and dominant inheritance patterns.
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Affiliation(s)
- Gesa Trieschmann
- Specialist Centre for Paediatric Neurology, Neurorehabilitation and Epileptology, Schoen Clinic Vogtareuth, Vogtareuth, Germany
| | | | - Steffen Berweck
- Specialist Centre for Paediatric Neurology, Neurorehabilitation and Epileptology, Schoen Clinic Vogtareuth, Vogtareuth, Germany; LMU Hospital, Department of Pediatrics-Dr. von Hauner Childrens's Hospital, Division of Pediatric Neurology and Developmental Medicine, Ludwig-Maximilians University, Munich, Germany
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.
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12
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Miao C, Du L, Zhang Y, Jia F, Shan L. Novel de novo ZNF148 truncating variant causing autism spectrum disorder, attention deficit hyperactivity disorder, and intellectual disability. Clin Genet 2023; 103:364-368. [PMID: 36444493 DOI: 10.1111/cge.14272] [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: 09/10/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022]
Abstract
ZNF148 gene is a Krüppel-type transcription factor that has transcriptional regulatory function. Heterozygous variant in ZNF148 gene causes an intellectual disability syndrome characterized by global developmental delay, absence, or hypoplasia of corpus callosum, wide intracerebral ventricles, and dysmorphic facial features, while its associations with ASD and ADHD have not been reported. We report a new patient with intellectual disability, autism spectrum disorder (ASD) and attention-deficit hyperactivity disorder (ADHD). The patient had a novel heterozygous truncating variant c.1818dupC (p.Lys607Glnfs*11) in the ZNF148 gene. This variation produces a ZNF148 truncated protein with a deletion of the C-terminal activation domain and may destabilize the protein by affecting the transcriptional activation function. Brain MRI shows normal brain development. Here, we identify a novel ZNF148 heterozygous truncating variant in a patient with distinct phenotypes of ASD and ADHD, which expands the genotype-phenotype spectrum of ZNF148, and indicates ZNF148 is also a potential target gene for ASD.
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Affiliation(s)
- Chunyue Miao
- Department of Developmental and Behavioral Pediatrics, The First Hospital of Jilin University, Jilin, China
| | - Lin Du
- Department of Developmental and Behavioral Pediatrics, The First Hospital of Jilin University, Jilin, China
| | - Yu Zhang
- Department of Developmental and Behavioral Pediatrics, The First Hospital of Jilin University, Jilin, China
| | - Feiyong Jia
- Department of Developmental and Behavioral Pediatrics, The First Hospital of Jilin University, Jilin, China
| | - Ling Shan
- Department of Developmental and Behavioral Pediatrics, The First Hospital of Jilin University, Jilin, China
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13
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Fabiani M, Libotte F, Margiotti K, Tannous DKI, Sparacino D, D’Aleo MP, Monaco F, Dello Russo C, Mesoraca A, Giorlandino C. Agnathia-Otocephaly Complex Due to a De Novo Deletion in the OTX2 Gene. Genes (Basel) 2022; 13:genes13122269. [PMID: 36553536 PMCID: PMC9778614 DOI: 10.3390/genes13122269] [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] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022] Open
Abstract
Agnathia-otocephaly complex (AOC) is a rare and usually lethal malformation typically characterized by hypoplasia or the absence of the mandible, ventromedial and caudal displacement of the ears with or without the fusion of the ears, a small oral aperture with or without a tongue hypoplasia. Its incidence is reported as 1 in 70,000 births and its etiology has been attributed to both genetic and teratogenic causes. AOC is characterized by a wide severity clinical spectrum even when occurring within the same family, ranging from a mild mandibular defect to an extreme facial aberration incompatible with life. Most AOC cases are due to a de novo sporadic mutation. Given the genetic heterogeneity, many genes have been reported to be implicated in this disease but to date, the link to only two genes has been confirmed in the development of this complex: the orthodenticle homeobox 2 (OTX2) gene and the paired related homeobox 1 (PRRX1) gene. In this article, we report a case of a fetus with severe AOC, diagnosed in routine ultrasound scan in the first trimester of pregnancy. The genetic analysis showed a novel 10 bp deletion mutation c.766_775delTTGGGTTTTA in the OTX2 gene, which has never been reported before, together with a missense variant c.778T>C in cis conformation.
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Affiliation(s)
- Marco Fabiani
- ALTAMEDICA, Human Genetics Laboratory, Viale Liegi 45, 00198 Rome, Italy
| | - Francesco Libotte
- ALTAMEDICA, Human Genetics Laboratory, Viale Liegi 45, 00198 Rome, Italy
| | - Katia Margiotti
- ALTAMEDICA, Human Genetics Laboratory, Viale Liegi 45, 00198 Rome, Italy
- Correspondence: ; Tel.: +39-06-85058961
| | - Dina Khader Issa Tannous
- School of Medicine and Surgery, Department of Obstetrics and Gynecology, UniCamillus-Saint Camillus International University of Health Sciences, Via di Sant’Alessandro, 8, 00131 Rome, Italy
| | - Davide Sparacino
- ALTAMEDICA, Human Genetics Laboratory, Viale Liegi 45, 00198 Rome, Italy
| | - Maria Pia D’Aleo
- ALTAMEDICA, Human Genetics Laboratory, Viale Liegi 45, 00198 Rome, Italy
| | - Francesca Monaco
- ALTAMEDICA, Human Genetics Laboratory, Viale Liegi 45, 00198 Rome, Italy
| | | | - Alvaro Mesoraca
- ALTAMEDICA, Human Genetics Laboratory, Viale Liegi 45, 00198 Rome, Italy
| | - Claudio Giorlandino
- ALTAMEDICA, Human Genetics Laboratory, Viale Liegi 45, 00198 Rome, Italy
- ALTAMEDICA, Department of Prenatal Diagnosis, Fetal-Maternal Medical Centre, Altamedica Viale Liegi 45, 00198 Rome, Italy
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14
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Abdel-Salam GM, Afifi HH, Saleem SN, Gadelhak MI, El-Serafy MA, Sayed IS, Abdel-Hamid MS. Further Evidence of a Continuum in the Clinical Spectrum of Dominant PIEZO2-Related Disorders and Implications in Cerebellar Anomalies. Mol Syndromol 2022; 13:389-396. [PMID: 36588752 PMCID: PMC9801318 DOI: 10.1159/000523956] [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: 01/09/2022] [Accepted: 03/03/2022] [Indexed: 01/04/2023] Open
Abstract
Introduction Pathogenic variants in the PIEZO family member 2 (PIEZO2) gene are known to cause Gordon syndrome (GS), Marden-Walker syndrome (MWS), and distal arthrogryposis type 5 (DA5). Out of these, MWS has a recognizable phenotype that can be discerned easily, but the distinction between GS and DA5 is less evident. Few children with pathogenic PIEZO2 variants have been reported to show posterior fossa anomalies. Methods and Results By candidate gene targeting guided by proper clinical evaluation and neuroimaging findings, a patient with classic MWS harboring a de novo novel variant (c.8237G>A, p.W2746*) in the C-terminal region of PIEZO2 was identified. In addition, another girl with the typical clinical features of GS is also described carrying the most prevalent reported variant (c.8057G>A, p.R2686H) in PIEZO2. The brain MRI of the 2 patients showed Dandy-Walker malformation (DWM). Diffusion tensor imaging visualized anteroposterior and downward aligned thin middle cerebellar peduncle. The association of DWM with arthrogryposis in the presence of PIEZO2 variants remains quite interesting and provides more evidence that PIEZO2 plays a role in the development of hindbrain although the underlying mechanism remains unclear. Moreover, the 2 girls had distinct foot patterning in the form of shortening of the first and fifth toes. Conclusion Phenotype analysis and a comprehensive review of the literature strongly support the previously published data and corroborate the evidence that heterozygous PIEZO2-related disorders represent a continuum with overlapping phenotypic features.
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Affiliation(s)
- Ghada M.H. Abdel-Salam
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt,*Ghada M.H. Abdel-Salam,
| | - Hanan H. Afifi
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | | | - Mohamed I. Gadelhak
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Manar A. El-Serafy
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Inas S.M. Sayed
- Orodental Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Mohamed S. Abdel-Hamid
- Medical Molecular Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
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15
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Chen M, Shen MC, Chang SP, Ma GC, Huang YC, Lin CY. Origin and timing of de novo variants implicated in type 2 von Willebrand disease. J Cell Mol Med 2022; 26:5403-5413. [PMID: 36226571 PMCID: PMC9639050 DOI: 10.1111/jcmm.17563] [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: 06/23/2022] [Revised: 08/30/2022] [Accepted: 09/11/2022] [Indexed: 12/03/2022] Open
Abstract
Very few studies have shown the real origin and timing of de novo variants (DNV) implicated in von Willebrand disease (VWD). We investigated four families with type 2 VWD. First, we conducted linkage analysis using single nucleotide variant genotyping to recognize the possible provenance of DNV. Second, we performed amplification refractory mutation system‐quantitative polymerase chain reaction to confirm the real origin of variant (~0% mutant cells) or presence of a genetic mosaic variant (0%–50% mutant cells) in three embryonic germ layer‐derived tissues and sperm cells. Then, three possible timings of DNV were categorized based on the relative likelihood of occurrence according to the number of cell divisions during embryogenesis. Two each with type 2B VWD (proband 1 p.Arg1308Cys, proband 4 p.Arg1306Trp) and type 2A VWD (proband 2 p.Leu1276Arg, proband 3 p.Ser1506Leu) were identified. Variant origins were identified for families 1, 2 and 3 and confirmed to originate from the mother, father and father, respectively. However, the father of family 4 was confirmed to have isolated germline mosaicism with 2.2% mutant sperm cells. Further investigation confirmed the paternal grandfather to be the origin of variant. Thus, we proposed that DNV originating from the two fathers most likely occurred at the single sperm cell, the one originating from the mother occurred at the zygote during the first few cellular divisions; alternatively, in family 4, the DNV most likely occurred at the early postzygotic development in the father. Our findings are essential for understanding genetic pathogenesis and providing accurate genetic counselling.
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Affiliation(s)
- Ming Chen
- Department of Genomic Medicine, Changhua Christian Hospital, Changhua, Taiwan.,Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
| | - Ming-Ching Shen
- Department of Internal Medicine, Changhua Christian Hospital, Changhua, Taiwan.,Department of Laboratory Medicine and Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Shun-Ping Chang
- Department of Genomic Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | - Gwo-Chin Ma
- Department of Genomic Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | - Ying-Chih Huang
- Department of Internal Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | - Ching-Yeh Lin
- Department of Internal Medicine, Changhua Christian Hospital, Changhua, Taiwan
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16
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Jaouadi H, El Louali F, Wanert C, Cano A, Ovaert C, Zaffran S. Dilated-Left Ventricular Non-Compaction Cardiomyopathy in a Pediatric Case with SPEG Compound Heterozygous Variants. Int J Mol Sci 2022; 23:5205. [PMID: 35563595 DOI: 10.3390/ijms23095205] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 04/08/2022] [Revised: 04/29/2022] [Accepted: 05/04/2022] [Indexed: 02/01/2023] Open
Abstract
Left Ventricular Non-Compaction (LVNC) is defined by the triad prominent myocardial trabecular meshwork, thin compacted layer, and deep intertrabecular recesses. LVNC associated with dilation is characterized by the coexistence of left ventricular dilation and systolic dysfunction. Pediatric cases with dilated-LVNC have worse outcomes than those with isolated dilated cardiomyopathy and adult patients. Herein, we report a clinical and genetic investigation using trio-based whole-exome sequencing of a pediatric case with early-onset dilated-LVNC. Compound heterozygous mutations were identified in the Striated Muscle Enriched Protein Kinase (SPEG) gene, a key regulator of cardiac calcium homeostasis. A paternally inherited mutation: SPEG; p.(Arg2470Ser) and the second variant, SPEG; p.(Pro2687Thr), is common and occurred de novo. Subsequently, Sanger sequencing was performed for the family in order to segregate the variants. Thus, the index case, his father, and both sisters carried the SPEG: p.(Arg2470Ser) variant. Only the index patient carried both SPEG variants. Both sisters, as well as the patient’s father, showed LVNC without cardiac dysfunction. The unaffected mother did not harbor any of the variants. The in silico analysis of the identified variants (rare and common) showed a decrease in protein stability with alterations of the physical properties as well as high conservation scores for the mutated residues. Interestingly, using the Project HOPE tool, the SPEG; p.(Pro2687Thr) variant is predicted to disturb the second fibronectin type III domain of the protein and may abolish its function. To our knowledge, the present case is the first description of compound heterozygous SPEG mutations involving a de novo variant and causing dilated-LVNC without neuropathy or centronuclear myopathy.
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17
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Liu Y, Zhang Q, Wang J, Liu J, Yang W, Yan X, Ouyang Y, Yang H. Both subthalamic and pallidal deep brain stimulation are effective for GNAO1-associated dystonia: three case reports and a literature review. Ther Adv Neurol Disord 2022; 15:17562864221093507. [PMID: 35509770 PMCID: PMC9058460 DOI: 10.1177/17562864221093507] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 03/24/2022] [Indexed: 11/16/2022] Open
Abstract
Background Mutations in the G-protein subunit alpha o1 (GNAO1) gene have recently been shown to be involved in the pathogenesis of early infantile epileptic encephalopathy and movement disorders. The clinical manifestations of GNAO1-associated movement disorders are highly heterogeneous. However, the genotype-phenotype correlations in this disease remain unclear, and the treatments for GNAO1-associated movement disorders are still limited. Objective The objective of this study was to explore diagnostic and therapeutic strategies for GNAO1-associated movement disorders. Methods This study describes the cases of three Chinese patients who had shown severe and progressive dystonia in the absence of epilepsy since early childhood. We performed genetic analyses in these patients. Patients 1 and 2 underwent globus pallidus internus (GPi) deep brain stimulation (DBS) implantation, and Patient 3 underwent subthalamic nucleus (STN) DBS implantation. In addition, on the basis of a literature review, we summarized and discussed the clinical characteristics and outcomes after DBS surgery for all reported patients with GNAO1-associated movement disorders. Results Whole-exome sequencing (WES) analysis revealed de novo variants in the GNAO1 gene for all three patients, including a splice-site variant (c.724-8G > A) in Patients 1 and 3 and a novel heterozygous missense variant (c.124G > A; p. Gly42Arg) in Patient 2. Both GPi and STN DBS were effective in improving the dystonia symptoms of all three patients. Conclusion DBS is effective in ameliorating motor symptoms in patients with GNAO1-associated movement disorders, and both STN DBS and GPi DBS should be considered promptly for patients with sustained refractory GNAO1-associated dystonia.
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Affiliation(s)
- Ye Liu
- Department of Neurology, The First Hospital of China Medical University, Shenyang, China
| | - Qingping Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Jun Wang
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
| | - Jiyuan Liu
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
| | - Wuyang Yang
- Department of Neurosurgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xuejing Yan
- Department of Neurology, The First Hospital of China Medical University, Shenyang, China
| | - Yi Ouyang
- Department of Neurology, The First Hospital of China Medical University, Shenyang 110001, Liaoning, China
| | - Haibo Yang
- Department of Pediatric Surgery, Peking University First Hospital, Beijing 100034, China
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18
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Yang Y, Zhang S, Yang W, Wei T, Hao W, Cheng T, Wang J, Dong W, Qian N. Case Report: Identification of a De novo C19orf12 Variant in a Patient With Mitochondrial Membrane Protein-Associated Neurodegeneration. Front Genet 2022; 13:852374. [PMID: 35432442 PMCID: PMC9006254 DOI: 10.3389/fgene.2022.852374] [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: 01/11/2022] [Accepted: 02/18/2022] [Indexed: 11/24/2022] Open
Abstract
Background: Mitochondrial membrane protein–associated neurodegeneration (MPAN) mostly arises as an autosomal recessive disease and is caused by variants in the chromosome 19 open reading frame 12 (C19orf12) gene. However, a few C19orf12 monoallelic truncating de novo variants have been reported and segregated as autosomal dominant traits in some cases. Methods: We performed whole-exome sequencing and analyzed genes related to neurodegeneration associated with brain iron accumulation for pathogenic variants. The identified variants were confirmed by Sanger sequencing and tested using in silico tools. Results: The patient had an onset of depression at the age of 22 years, which rapidly progressed to severe dystonia, dementia, and bladder and bowel incontinence. Neuroimaging showed hypointensity in the substantia nigra and the globus pallidum, with additional frontotemporal atrophy. Genetic analysis revealed a single complex de novo variant [c.336_338delinsCACA (p.Trp112CysfsTer40)] in the C19orf12 gene. Conclusion: This study enriches the genetic spectrum and clinical features of C19orf12 variants and provides additional evidence of the variable inheritance pattern of MPAN.
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Affiliation(s)
- Yue Yang
- Graduate School of Anhui University of Chinese Medicine, Hefei, China
| | - Shijie Zhang
- The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Wenming Yang
- The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.,Xin'an Medical Education Ministry Key Laboratory, Hefei, China
| | - Taohua Wei
- The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Wenjie Hao
- Graduate School of Anhui University of Chinese Medicine, Hefei, China
| | - Ting Cheng
- Clinical School of Anhui Medical University, Hefei, China
| | - Jiuxiang Wang
- The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Wei Dong
- Graduate School of Anhui University of Chinese Medicine, Hefei, China.,The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Nannan Qian
- Graduate School of Anhui University of Chinese Medicine, Hefei, China
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19
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Itai T, Wang Z, Nishimura G, Ohashi H, Guo L, Wakano Y, Sugiura T, Hayakawa H, Okada M, Saisu T, Kitta A, Doi H, Kurosawa K, Hotta Y, Hosono K, Sato M, Shimizu K, Takikawa K, Watanabe S, Ikeda N, Suzuki M, Fujita A, Uchiyama Y, Tsuchida N, Miyatake S, Miyake N, Matsumoto N, Ikegawa S. De novo heterozygous variants in KIF5B cause kyphomelic dysplasia. Clin Genet 2022; 102:3-11. [PMID: 35342932 DOI: 10.1111/cge.14133] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 11/29/2022]
Abstract
Kyphomelic dysplasia is a heterogeneous group of skeletal dysplasias characterized by severe bowing of the limbs associated with other variable findings, such as narrow thorax and abnormal facies. We searched for the genetic etiology of this disorder. Four individuals diagnosed with kyphomelic dysplasia were enrolled. We performed whole-exome sequencing and evaluated the pathogenicity of the identified variants. All individuals had de novo heterozygous variants in KIF5B encoding kinesin-1 heavy chain: two with c.272A>G:p.(Lys91Arg), one with c.584C>A:p.(Thr195Lys), and the other with c.701G>T:p.(Gly234Val). All variants involved conserved amino acids in or close to the ATPase activity-related motifs in the catalytic motor domain of the KIF5B protein. All individuals had sharp angulation of the femora and humeri, distinctive facial features, and neonatal respiratory distress. Short stature was observed in three individuals. Three developed postnatal osteoporosis with subsequent fractures, two showed brachycephaly, and two were diagnosed with optic atrophy. Our findings suggest that heterozygous KIF5B deleterious variants cause a specific form of kyphomelic dysplasia. Furthermore, alterations in kinesins cause various symptoms known as kinesinopathies, and our findings also extend the phenotypic spectrum of kinesinopathies. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Toshiyuki Itai
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Zheng Wang
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Minato-ku, Tokyo, Japan
| | - Gen Nishimura
- Center for Intractable Diseases, Saitama Medical University Hospital, Moroyama, Iruma-gun, Saitama, Japan
| | - Hirofumi Ohashi
- Division of Medical Genetics, Saitama Children's Medical Center, Saitama, Saitama, Japan
| | - Long Guo
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Minato-ku, Tokyo, Japan
| | - Yasuhiro Wakano
- Department of Pediatrics, Toyohashi Municipal Hospital, Toyohashi, Aichi, Japan
| | - Takahiro Sugiura
- Department of Pediatrics, Toyohashi Municipal Hospital, Toyohashi, Aichi, Japan
| | - Hiromi Hayakawa
- Department of Obstetrics, Aichi Children's Health and Medical Center, Obu, Aichi, Japan
| | - Mayumi Okada
- Department of Obstetrics and Gynecology, Genome Medical Center, Toyohashi Municipal Hospital, Toyohashi, Aichi, Japan
| | - Takashi Saisu
- Chiba Child & Adult Orthopaedic Clinic, Chiba, Chiba, Japan
| | - Ayana Kitta
- Department of Orthopedic Surgery, Tokyo Women's Medical University, Yachiyo Medical Center, Yachiyo, Chiba, Japan
| | - Hiroshi Doi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Kanagawa, Japan
| | - Yoshihiro Hotta
- Department of Ophthalmology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Katsuhiro Hosono
- Department of Ophthalmology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Miho Sato
- Department of Ophthalmology, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Kenji Shimizu
- Division of Clinical Genetics and Cytogenetics, Shizuoka Children's Hospital, Shizuoka, Shizuoka, Japan
| | - Kazuharu Takikawa
- Department of Pediatric Orthopedics, Shizuoka Children's Hospital, Shizuoka, Shizuoka, Japan
| | - Seiji Watanabe
- Department of Pediatrics, Izu Medical and Welfare Center, Izunokuni, Shizuoka, Japan
| | - Naho Ikeda
- Department of Neonatology, Juntendo University Shizuoka Hospital, Izunokuni, Shizuoka, Japan
| | - Mitsuyoshi Suzuki
- Department of Pediatrics, Juntendo University Faculty of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Kanagawa, Japan
| | - Noriko Miyake
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Minato-ku, Tokyo, Japan
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20
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Wang K, Zhao S, Xie Z, Zhang M, Zhao H, Cheng X, Zhang Y, Niu Y, Liu J, Zhang TJ, Zhang Y, Wu Z, Chu J, Yang X, Wu N. Exome-wide Analysis of De Novo and Rare Genetic Variants in Patients With Brain Arteriovenous Malformation. Neurology 2022; 98:e1670-e1678. [PMID: 35228337 DOI: 10.1212/wnl.0000000000200114] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 01/11/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Brain arteriovenous malformation (bAVM) is a congenital disorder and a leading cause of hemorrhagic stroke. Germline genetic variants play an essential role in the pathogenesis of brain arteriovenous malformation. However, the biological relevance of the disease-associated genes identified in previous studies is elusive. In this study, we aim to systematically investigate the contribution of germline variants to bAVM and explore the critical molecular pathways underlying the pathogenesis of bAVM. METHODS Probands with sporadic bAVM were consecutively recruited into this study from November 2015 to November 2018 and underwent exome sequencing. The controls were aggregated from individuals who were not known to have vascular malformation and underwent exome sequencing for clinical or research purposes. The retained control dataset included 4609 individuals, including 251 individuals with parental samples sequenced. We firstly compared de novo variants in cases and controls and performed a pathway enrichment analysis. A gene-based rare variant association analysis was then performed to identify genes whose variants were significantly enriched in cases. RESULTS We collected an exome-sequenced bAVM cohort consisting of 152 trios and 40 singletons. By firstly focusing on de novo variants, we observed a significant mutational burden of de novo likely gene-disrupting variants in cases versus controls. By performing a pathway enrichment analysis of all nonsynonymous de novo variants identified in cases, we found the angiopoietin-like protein 8 (ANGPTL8) regulatory pathway to be significantly enriched in patients with bAVM. Through an exome-wide rare variant association analysis utilizing 4394 in-house exome data as controls, we identified SLC19A3 as a disease-associated gene for bAVM. In addition, we found that the SLC19A3 variants in cases are preferably located at the N' side of the SLC19A3 protein. These findings implicate a phenotypic extension of SLC19A3-related disorders with a domain-specific effect. DISCUSSION This study provides insights into the biological basis of bAVM by identifying novel molecular pathways and candidate genes.
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Affiliation(s)
- Kun Wang
- Department of Interventional Neuroradiology, Beijing Tiantan Hospital, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Sen Zhao
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, 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
| | - Zhixin Xie
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, 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
| | - Mingqi Zhang
- Department of Interventional Neuroradiology, Beijing Tiantan Hospital, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Hengqiang Zhao
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, 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
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, 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
| | - Yisen Zhang
- Department of Interventional Neuroradiology, Beijing Tiantan Hospital, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jian Liu
- Department of Interventional Neuroradiology, Beijing Tiantan Hospital, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Terry Jianguo Zhang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, 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
| | - Ying Zhang
- Department of Interventional Neuroradiology, Beijing Tiantan Hospital, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Junsheng Chu
- Department of Neurosurgery, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Xinjian Yang
- Department of Interventional Neuroradiology, Beijing Tiantan Hospital, Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Nan Wu
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Orthopedic Surgery, 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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21
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Frisk S, Wachtmeister A, Laurell T, Lindstrand A, Jäntti N, Malmgren H, Lagerstedt-Robinson K, Tesi B, Taylan F, Nordgren A. Detection of germline mosaicism in fathers of children with intellectual disability syndromes caused by de novo variants. Mol Genet Genomic Med 2022; 10:e1880. [PMID: 35118825 PMCID: PMC9000944 DOI: 10.1002/mgg3.1880] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 09/10/2021] [Revised: 12/21/2021] [Accepted: 01/14/2022] [Indexed: 12/03/2022] Open
Abstract
Background De novo variants are a common cause to rare intellectual disability syndromes, associated with low recurrence risk. However, when such variants occur pre‐zygotically in parental germ cells, the recurrence risk might be higher. Still, the recurrence risk estimates are mainly based on empirical data and the prevalence of germline mosaicism is often unknown. Methods To establish the prevalence of mosaicism in parents of children with intellectual disability syndromes caused by de novo variants, we performed droplet digital PCR on DNA extracted from blood (43 trios), and sperm (31 fathers). Results We detected low‐level mosaicism in sperm‐derived DNA but not in blood in the father of a child with Kleefstra syndrome caused by an EHMT1 variant. Additionally, we found a higher level of paternal mosaicism in sperm compared to blood in the father of a child with Gillespie syndrome caused by an ITPR1 variant. Conclusion By employing droplet digital PCR, we detected paternal germline mosaicism in two intellectual disability syndromes. In both cases, the mosaicism level was higher in sperm than blood, indicating that analysis of blood alone may underestimate germline mosaicism. Therefore, sperm analysis can be clinically useful to establish the recurrence risk for parents and improve genetic counselling.
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Affiliation(s)
- Sofia Frisk
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Alexandra Wachtmeister
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Tobias Laurell
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Hand Surgery, Södersjukhuset, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Nina Jäntti
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Helena Malmgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Kristina Lagerstedt-Robinson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Bianca Tesi
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
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22
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Lei M, Wang P, Li H, Liu X, Shu J, Zhang Q, Cai C, Li D, Zhang Y. Case Report: Recurrent Hemiplegic Migraine Attacks Accompanied by Intractable Hypomagnesemia Due to a de novo TRPM7 Gene Variant. Front Pediatr 2022; 10:880242. [PMID: 35712613 PMCID: PMC9194527 DOI: 10.3389/fped.2022.880242] [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: 02/21/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Transient receptor potential melastatin 7 (TRPM7) is a ubiquitously expressed chanzyme comprised of a divalent cation channel permeable to calcium and magnesium and a cytosolic serine-threonine α-kinase domain. TRPM7 has a crucial role in magnesium ion homeostasis and anoxic neuronal death, which was identified as a potential non-glutamate target for hypoxic-ischemic neuronal injury. TRPM7 is implicated in ischemic stroke and hypomagnesemia in many studies, but it has not been associated with disease in the OMIM database. No clinical cases between TRPM7 gene variants and hypomagnesemia have been reported, so far. One patient with recurrent hemiplegic migraine attacks accompanied by intractable hypomagnesemia was followed up at Tianjin Children's Hospital from 2018 to 2021. We systematically summarized and analyzed the clinical manifestations, imaging features, and serum magnesium changes of the patient. Genetic analysis was performed by whole-exome sequencing and Sanger sequencing to infer the etiology of hemiplegic migraine attacks and hypomagnesemia in this patient. Gene sequencing revealed a novel heterozygous variant of the TRPM7 gene (c.2998A>G, p. Met1000Val), which has not been reported previously; this is also a de novo variant that is not inherited from his parents. We described a novel variant p. Met1000Val (c.2998A>G) located in the transmembrane region of TRPM7 protein, which is possibly crucial for the normal function of the ion channel. Our study expands the variation spectrum of the TRPM7 gene, highlights the importance of molecular genetic evaluation in patients with TRPM7 gene deficiency, and demonstrates the causal relationship between TRPM7 gene variants and disease manifestations.
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Affiliation(s)
- Meifang Lei
- Department of Neurology, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
| | - Ping Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Hong Li
- Department of Neurology, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
| | - Xiaojun Liu
- Department of Neurology, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
| | - Jianbo Shu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Qianqian Zhang
- Department of Neurology, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
| | - Chunquan Cai
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China.,Department of Neurosurgery, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
| | - Dong Li
- Department of Neurology, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
| | - Yuqin Zhang
- Department of Neurology, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
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Kim SH, Kwon SS, Lee JS, Kim HD, Lee ST, Choi JR, Shin S, Kang HC. Analysis of trio test in neurodevelopmental disorders. Front Pediatr 2022; 10:1073083. [PMID: 36619507 PMCID: PMC9816327 DOI: 10.3389/fped.2022.1073083] [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: 10/18/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Trio test has been widely used for diagnosis of various hereditary disorders. We aimed to investigate the contribution of trio test in genetically diagnosing neurodevelopmental disorders (NDD). METHODS We retrospectively reviewed 2,059 NDD cases with genetic test results. The trio test was conducted in 563 cases. Clinical usefulness, optimal timing, and methods for the trio test were reviewed. RESULTS Pathogenic or likely pathogenic variants were detected in 112 of 563 (19.9%) patients who underwent the trio test. With trio test results, the overall diagnostic yield increased by 5.4% (112/2,059). Of 165 de novo variants detected, 149 were pathogenic and we detected 85 novel pathogenic variants. Pathogenic, de novo variants were frequently detected in CDKL5, ATP1A3, and STXBP1. CONCLUSION The trio test is an efficient method for genetically diagnosing NDD. We identified specific situations where a certain trio test is more appropriate, thereby providing a guide for clinicians when confronted with variants of unknown significance of specific genes.
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Affiliation(s)
- Se Hee Kim
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, South Korea
| | - Soon Sung Kwon
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Joon Soo Lee
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, South Korea
| | - Heung Dong Kim
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, South Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Hoon-Chul Kang
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, South Korea
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24
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Huang TX, Ma GC, Chen M, Li WF, Shaw SW. Difficulties of Prenatal Genetic Counseling for a Subsequent Child in a Family With Multiple Genetic Variations. Front Genet 2022; 12:612100. [PMID: 34970295 PMCID: PMC8712678 DOI: 10.3389/fgene.2021.612100] [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: 09/30/2020] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Many parents with a disabled child caused by a genetic condition appreciate the option of prenatal genetic diagnosis to understand the chance of recurrence in a future pregnancy. Genome-wide tests, such as chromosomal microarray analysis and whole-exome sequencing, have been increasingly used for prenatal diagnosis, but prenatal counseling can be challenging due to the complexity of genomic data. This situation is further complicated by incidental findings of additional genetic variations in subsequent pregnancies. Here, we report the prenatal identification of a baby with a MECP2 missense variant and 15q11.2 microduplication in a family that has had a child with developmental and epileptic encephalopathy caused by a de novo KCNQ2 variant. An extended segregation analysis including extended relatives, in addition to the parents, was carried out to provide further information for genetic counseling. This case illustrates the challenges of prenatal counseling and highlights the need to understand the clinical and ethical implications of genome-wide tests.
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Affiliation(s)
- Ting-Xuan Huang
- Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Gwo-Chin Ma
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua, Taiwan
| | - Ming Chen
- Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua, Taiwan.,Department of Obstetrics and Gynecology, Changhua Christian Hospital, Changhua, Taiwan.,Department of Molecular Biotechnology, Da-Yeh University, Changhua, Taiwan.,Department of Obstetrics and Gynecology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.,Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Wen-Fang Li
- Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Steven W Shaw
- Department of Obstetrics and Gynecology, Taipei Chang Gung Memorial Hospital, Taipei, Taiwan.,College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Prenatal Cell and Gene Therapy Group, Institute for Women's Health University College London, London, United Kingdom
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25
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Shah J, Patel H, Jain D, Sheth F, Sheth H. A rare case of a male child with post-zygotic de novo mosaic variant c.538C > T in MECP2 gene: a case report of Rett syndrome. BMC Neurol 2021; 21:469. [PMID: 34856927 PMCID: PMC8638266 DOI: 10.1186/s12883-021-02500-5] [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: 10/02/2021] [Accepted: 11/21/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rett syndrome (RTT) is characterized by a normal perinatal period with a normal head size at birth followed by normal development for the first 6 months of life followed by gradual deceleration of head growth, loss of acquired purposeful hand skills, severe expressive and receptive language impairment, severe intellectual disability and gait and truncal apraxia/ ataxia. It is caused due to mutations in the MECP2 gene and follows an X-linked dominant mode of inheritance. It was observed exclusively in females and was believed to be lethal in males. In contrast to this belief, several males were identified with RTT upon genetic analysis, however, most males expired by the age of 2 years due to neonatal encephalopathy. The ones that survived beyond the age of 2 years, were attributed to the presence of an extra X chromosome (co-occurrence of Klinefelter and RTT) or the ones having mosaic cell lines. Only 11 males with somatic mosaicism are known till date. CASE PRESENTATION This case reports an ultra-rare case of a male affected with RTT surviving beyond the age of 2 years due to post-zygotic de novo somatic mosaicism. He was identified with a known pathogenic variant c.538C > T (p.R180*), which to the best of our knowledge is exclusively seen in females and has never been reported in a male before. CONCLUSION The present case is the first report of a mosaic male affected with RTT from India. The present report also carried out genotype-phenotype correlations across surviving mosaic males with RTT. We also postulate the effect of variant type, position along the gene and the variant allele fraction in different tissue types to be correlated with disease severity.
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Affiliation(s)
- Jhanvi Shah
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, 380015, Ahmedabad, India
| | | | - Deepika Jain
- Shishu Child Development and Early Intervention Centre, Ahmedabad, India
| | - Frenny Sheth
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, 380015, Ahmedabad, India.
| | - Harsh Sheth
- FRIGE's Institute of Human Genetics, FRIGE House, Jodhpur Gam Road, Satellite, 380015, Ahmedabad, India.
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26
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Luo S, Bi B, Zhang W, Zhou R, Chen W, Zhao P, Huang Y, Yuan L, He X. Three de novo variants in KMT2A (MLL) identified by whole exome sequencing in patients with Wiedemann-Steiner syndrome. Mol Genet Genomic Med 2021; 9:e1798. [PMID: 34469078 PMCID: PMC8580087 DOI: 10.1002/mgg3.1798] [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: 03/10/2021] [Revised: 07/17/2021] [Accepted: 08/16/2021] [Indexed: 11/26/2022] Open
Abstract
Background Wiedemann–Steiner syndrome (WSS) is an autosomal dominant disorder characterized by short stature, hypertrichosis, intellectual disability, developmental delay, along with facial dysmorphism. WSS patients exhibit great phenotypic heterogeneities. Some variants in KMT2A (MLL) gene have been identified as the cause of WSS. Methods Whole exome sequencing on the probands followed by Sanger sequencing validations in the family were applied to determine genetic variants. In silico analyses were used for predicting potential effects of the variants. Results We identified three novel de novo heterozygous variants: c.883A>T (p.Lys295*), c.4171C>T (p.Gln1391*), and c.3499T>C (p.Cys1167Arg), in KMT2A gene from three unrelated Chinese WSS patients. According to the American College of Medical Genetics and Genomics (ACMG) guidelines, these three variants were classified as pathogenic, pathogenic and likely pathogenic variant, respectively. By reviewing all the available cases with same mutated KMT2A regions as the three patients had, we found that in addition to the representative symptoms, our patients exhibited some sporadically observed symptoms, such as severe ophthalmological symptoms, endocardial fibroelastosis, cytomegalovirus infection, and feet eversion. We also revealed that variants in different KMT2A regions contribute to the phenotypic heterogeneity of WSS, highlighting challenges in the diagnosis of syndromic disorders spanning a broad phenotypic spectrum. Conclusion Our study would aid in further broadening our knowledge about the genotype–phenotype correlation of WSS.
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Affiliation(s)
- Sukun Luo
- Precision Medical Laboratory, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Bo Bi
- Rehabilitation Department, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Wenqian Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rui Zhou
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, China.,State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wei Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, China
| | - Peiwei Zhao
- Precision Medical Laboratory, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Yufeng Huang
- Precision Medical Laboratory, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Li Yuan
- Ultrasonography Department, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Xuelian He
- Precision Medical Laboratory, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
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Yanagishita T, Hirade T, Shimojima Yamamoto K, Funatsuka M, Miyamoto Y, Maeda M, Yanagi K, Kaname T, Nagata S, Nagata M, Ishihara Y, Miyashita Y, Asano Y, Sakata Y, Kosaki K, Yamamoto T. HECW2-related disorder in four Japanese patients. Am J Med Genet A 2021; 185:2895-2902. [PMID: 34047014 DOI: 10.1002/ajmg.a.62363] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/14/2021] [Accepted: 05/09/2021] [Indexed: 11/11/2022]
Abstract
The HECT, C2, and WW domain containing E3 ubiquitin protein ligase 2 gene (HECW2) is involved in protein ubiquitination. Several genes associated with protein ubiquitination have been linked to neurodevelopmental disorders. HECW2-related disorder has been established through the identification of de novo variants in HECW2 in patients with neurodevelopmental disorders with hypotonia, seizures, and absent language. Recently, we identified novel HECW2 variants in four Japanese patients with neurodevelopmental disorders. Regarding motor development, two of the patients cannot walk, whereas the other two can walk with an unsteady gait, owing to hypotonia. All HECW2 variants, including those that were previously reported, are missense, and no loss-of-function variants have been identified. Most of the identified variants are located around the HECT domain. These findings suggest that the dominant negative effects of missense variants around the HECT domain may be the mechanism underlying HECW2-related disorder.
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Affiliation(s)
- Tomoe Yanagishita
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Takuya Hirade
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Keiko Shimojima Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan.,Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
| | - Makoto Funatsuka
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Yusaku Miyamoto
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Makiko Maeda
- Department of Pediatrics, Saga Medical and Welfare Center for the Challenged, Saga, Japan
| | - Kumiko Yanagi
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Tadashi Kaname
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Satoru Nagata
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Miho Nagata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yasuki Ishihara
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yohei Miyashita
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan.,Department of Legal Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yoshihiro Asano
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yasushi Sakata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
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Epilepsy Phenome/Genome Project, Epi4K Consortium. Diverse genetic causes of polymicrogyria with epilepsy. Epilepsia 2021; 62:973-83. [PMID: 33818783 DOI: 10.1111/epi.16854] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 12/25/2022]
Abstract
OBJECTIVE We sought to identify novel genes and to establish the contribution of known genes in a large cohort of patients with nonsyndromic sporadic polymicrogyria and epilepsy. METHODS We enrolled participants with polymicrogyria and their parents through the Epilepsy Phenome/Genome Project. We performed phenotyping and whole exome sequencing (WES), trio analysis, and gene-level collapsing analysis to identify de novo or inherited variants, including germline or mosaic (postzygotic) single nucleotide variants, small insertion-deletion (indel) variants, and copy number variants present in leukocyte-derived DNA. RESULTS Across the cohort of 86 individuals with polymicrogyria and epilepsy, we identified seven with pathogenic or likely pathogenic variants in PIK3R2, including four germline and three mosaic variants. PIK3R2 was the only gene harboring more than expected de novo variants across the entire cohort, and likewise the only gene that passed the genome-wide threshold of significance in the gene-level rare variant collapsing analysis. Consistent with previous reports, the PIK3R2 phenotype consisted of bilateral polymicrogyria concentrated in the perisylvian region with macrocephaly. Beyond PIK3R2, we also identified one case each with likely causal de novo variants in CCND2 and DYNC1H1 and biallelic variants in WDR62, all genes previously associated with polymicrogyria. Candidate genetic explanations in this cohort included single nucleotide de novo variants in other epilepsy-associated and neurodevelopmental disease-associated genes (SCN2A in two individuals, GRIA3, CACNA1C) and a 597-kb deletion at 15q25, a neurodevelopmental disease susceptibility locus. SIGNIFICANCE This study confirms germline and postzygotically acquired de novo variants in PIK3R2 as an important cause of bilateral perisylvian polymicrogyria, notably with macrocephaly. In total, trio-based WES identified a genetic diagnosis in 12% and a candidate diagnosis in 6% of our polymicrogyria cohort. Our results suggest possible roles for SCN2A, GRIA3, CACNA1C, and 15q25 deletion in polymicrogyria, each already associated with epilepsy or other neurodevelopmental conditions without brain malformations. The role of these genes in polymicrogyria will be further understood as more patients with polymicrogyria undergo genetic evaluation.
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29
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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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30
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Li K, Ling Z, Luo T, Zhao G, Zhou Q, Wang X, Xia K, Li J, Li B. Cross-Disorder Analysis of De Novo Variants Increases the Power of Prioritising Candidate Genes. Life (Basel) 2021; 11:life11030233. [PMID: 33809095 PMCID: PMC8001830 DOI: 10.3390/life11030233] [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: 01/29/2021] [Revised: 03/01/2021] [Accepted: 03/06/2021] [Indexed: 11/16/2022] Open
Abstract
De novo variants (DNVs) are critical to the treatment of neurodevelopmental disorders (NDDs). However, effectively identifying candidate genes in small cohorts is challenging in most NDDs because of high genetic heterogeneity. We hypothesised that integrating DNVs from multiple NDDs with genetic similarity can significantly increase the possibility of prioritising the candidate gene. We catalogued 66,186 coding DNVs in 50,028 individuals with nine types of NDDs in cohorts with sizes spanning from 118 to 31,260 from Gene4Denovo database to validate this hypothesis. Interestingly, we found that integrated DNVs can effectively increase the number of prioritised candidate genes for each disorder. We identified 654 candidate genes including 481 shared candidate genes carrying putative functional variants in at least two disorders. Notably, 13.51% (65/481) of shared candidate genes were prioritised only via integrated analysis including 44.62% (29/65) genes validated in recent large cohort studies. Moreover, we estimated that more novel candidate genes will be prioritised with the increase in cohort size, in particular for some disorders with high putative functional DNVs per individual. In conclusion, integrated DNVs may increase the power of prioritising candidate genes, which is important for NDDs with small cohort size.
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Affiliation(s)
- Kuokuo Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China; (K.L.); (G.Z.); (Q.Z.)
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei 230022, China
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China; (Z.L.); (T.L.); (X.W.); (K.X.)
| | - Zhengbao Ling
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China; (Z.L.); (T.L.); (X.W.); (K.X.)
| | - Tengfei Luo
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China; (Z.L.); (T.L.); (X.W.); (K.X.)
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China; (K.L.); (G.Z.); (Q.Z.)
| | - Qiao Zhou
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China; (K.L.); (G.Z.); (Q.Z.)
| | - Xiaomeng Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China; (Z.L.); (T.L.); (X.W.); (K.X.)
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China; (Z.L.); (T.L.); (X.W.); (K.X.)
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China; (K.L.); (G.Z.); (Q.Z.)
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China; (Z.L.); (T.L.); (X.W.); (K.X.)
- Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
- Correspondence: (J.L.); (B.L.); Tel.: +86-731-8975-2406 (J.L. & B.L.); Fax: +86-731-8432-7332 (J.L. & B.L.)
| | - Bin Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China; (K.L.); (G.Z.); (Q.Z.)
- Mobile Health Ministry of Education—China Mobile Joint Laboratory, Xiangya Hospital, Central South University, Changsha 410008, China
- Correspondence: (J.L.); (B.L.); Tel.: +86-731-8975-2406 (J.L. & B.L.); Fax: +86-731-8432-7332 (J.L. & B.L.)
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31
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Tian T, Cao X, Chen Y, Jin L, Li Z, Han X, Lin Y, Wlodarczyk BJ, Finnell RH, Yuan Z, Wang L, Ren A, Lei Y. Somatic and de novo Germline Variants of MEDs in Human Neural Tube Defects. Front Cell Dev Biol 2021; 9:641831. [PMID: 33748132 PMCID: PMC7969791 DOI: 10.3389/fcell.2021.641831] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 12/15/2020] [Accepted: 02/15/2021] [Indexed: 02/05/2023] Open
Abstract
Background Neural tube defects (NTDs) are among the most common and severe congenital defects in humans. Their genetic etiology is complex and remains poorly understood. The Mediator complex (MED) plays a vital role in neural tube development in animal models. However, no studies have yet examined the role of its human homolog in the etiology of NTDs. Methods In this study, 48 pairs of neural lesion site and umbilical cord tissues from NTD and 21 case-parent trios were involved in screening for NTD-related somatic and germline de novo variants. A series of functional cell assays were performed. We generated a Med12 p.Arg1784Cys knock-in mouse using CRISPR/Cas9 technology to validate the human findings. Results One somatic variant, MED12 p.Arg1782Cys, was identified in the lesion site tissue from an NTD fetus. This variant was absent in any other normal tissue from different germ layers of the same case. In 21 case-parent trios, one de novo stop-gain variant, MED13L p.Arg1760∗, was identified. Cellular functional studies showed that MED12 p.Arg1782Cys decreased MED12 protein level and affected the regulation of MED12 on the canonical-WNT signaling pathway. The Med12 p.Arg1784Cys knock-in mouse exhibited exencephaly and spina bifida. Conclusion These findings provide strong evidence that functional variants of MED genes are associated with the etiology of some NTDs. We demonstrated a potentially important role for somatic variants in the occurrence of NTDs. Our study is the first study in which an NTD-related variant identified in humans was validated in mice using CRISPR/Cas9 technology.
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Affiliation(s)
- Tian Tian
- National Health Commission Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, Peking University, Beijing, China.,Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Xuanye Cao
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
| | - Yongyan Chen
- National Health Commission Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, Peking University, Beijing, China.,Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Lei Jin
- National Health Commission Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, Peking University, Beijing, China.,Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Zhiwen Li
- National Health Commission Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, Peking University, Beijing, China.,Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Xiao Han
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
| | - Ying Lin
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
| | - Bogdan J Wlodarczyk
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
| | - Richard H Finnell
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States.,Departments of Molecular and Human Genetics and Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Zhengwei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, China
| | - Linlin Wang
- National Health Commission Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, Peking University, Beijing, China.,Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Aiguo Ren
- National Health Commission Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, Peking University, Beijing, China.,Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Yunping Lei
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
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Brunet T, Jech R, Brugger M, Kovacs R, Alhaddad B, Leszinski G, Riedhammer KM, Westphal DS, Mahle I, Mayerhanser K, Skorvanek M, Weber S, Graf E, Berutti R, Necpál J, Havránková P, Pavelekova P, Hempel M, Kotzaeridou U, Hoffmann GF, Leiz S, Makowski C, Roser T, Schroeder SA, Steinfeld R, Strobl-Wildemann G, Hoefele J, Borggraefe I, Distelmaier F, Strom TM, Winkelmann J, Meitinger T, Zech M, Wagner M. De novo variants in neurodevelopmental disorders-experiences from a tertiary care center. Clin Genet 2021; 100:14-28. [PMID: 33619735 DOI: 10.1111/cge.13946] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 01/03/2023]
Abstract
Up to 40% of neurodevelopmental disorders (NDDs) such as intellectual disability, developmental delay, autism spectrum disorder, and developmental motor abnormalities have a documented underlying monogenic defect, primarily due to de novo variants. Still, the overall burden of de novo variants as well as novel disease genes in NDDs await discovery. We performed parent-offspring trio exome sequencing in 231 individuals with NDDs. Phenotypes were compiled using human phenotype ontology terms. The overall diagnostic yield was 49.8% (n = 115/231) with de novo variants contributing to more than 80% (n = 93/115) of all solved cases. De novo variants affected 72 different-mostly constrained-genes. In addition, we identified putative pathogenic variants in 16 genes not linked to NDDs to date. Reanalysis performed in 80 initially unsolved cases revealed a definitive diagnosis in two additional cases. Our study consolidates the contribution and genetic heterogeneity of de novo variants in NDDs highlighting trio exome sequencing as effective diagnostic tool for NDDs. Besides, we illustrate the potential of a trio-approach for candidate gene discovery and the power of systematic reanalysis of unsolved cases.
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Affiliation(s)
- Theresa Brunet
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Robert Jech
- Department of Neurology, Charles University, 1st Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic
| | - Melanie Brugger
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Human Genetics, University Hospital, Ludwig Maximilians University of Munich, Munich, Germany
| | - Reka Kovacs
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Bader Alhaddad
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Gloria Leszinski
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Korbinian M Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Dominik S Westphal
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Medical Department I, Cardiology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Isabella Mahle
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Katharina Mayerhanser
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Matej Skorvanek
- Department of Neurology, P. J. Safarik University, Kosice, Slovakia.,Department of Neurology, University Hospital L. Pasteur, Kosice, Slovakia
| | - Sandrina Weber
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.,Paracelsus-Elena-Klinik, Kassel, Germany
| | - Elisabeth Graf
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Riccardo Berutti
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Ján Necpál
- Department of Neurology, Zvolen Hospital, Zvolen, Slovakia
| | - Petra Havránková
- Department of Neurology, Charles University, 1st Faculty of Medicine and General University Hospital in Prague, Prague, Czech Republic
| | - Petra Pavelekova
- Department of Neurology, P. J. Safarik University, Kosice, Slovakia.,Department of Neurology, University Hospital L. Pasteur, Kosice, Slovakia
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Urania Kotzaeridou
- Division of Child Neurology and Inherited Metabolic Diseases, Centre for Paediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Georg F Hoffmann
- Division of Child Neurology and Inherited Metabolic Diseases, Centre for Paediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Steffen Leiz
- Divison of Neuropediatrics, Clinic for Children and Adolescents Dritter Orden, Munich, Germany
| | - Christine Makowski
- Department of Pediatrics, Technische Universität München, Munich, Germany
| | - Timo Roser
- Department of Paediatric Neurology and Developmental Medicine, Hauner Children's Hospital, University of Munich, Munich, Germany
| | - Sebastian A Schroeder
- Department of Paediatric Neurology and Developmental Medicine, Hauner Children's Hospital, University of Munich, Munich, Germany
| | - Robert Steinfeld
- Division of Pediatric Neurology, University Children's Hospital Zurich, Zurich, Switzerland
| | | | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Ingo Borggraefe
- Department of Paediatric Neurology and Developmental Medicine, Hauner Children's Hospital, University of Munich, Munich, Germany
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Tim M Strom
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Juliane Winkelmann
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,Neurogenetics, Technische Universität München, Munich, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Michael Zech
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Matias Wagner
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
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Itai T, Hamanaka K, Sasaki K, Wagner M, Kotzaeridou U, Brösse I, Ries M, Kobayashi Y, Tohyama J, Kato M, Ong WP, Chew HB, Rethanavelu K, Ranza E, Blanc X, Uchiyama Y, Tsuchida N, Fujita A, Azuma Y, Koshimizu E, Mizuguchi T, Takata A, Miyake N, Takahashi H, Miyagi E, Tsurusaki Y, Doi H, Taguri M, Antonarakis SE, Nakashima M, Saitsu H, Miyatake S, Matsumoto N. De novo variants in CELF2 that disrupt the nuclear localization signal cause developmental and epileptic encephalopathy. Hum Mutat 2020; 42:66-76. [PMID: 33131106 DOI: 10.1002/humu.24130] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 09/16/2020] [Accepted: 10/17/2020] [Indexed: 12/20/2022]
Abstract
We report heterozygous CELF2 (NM_006561.3) variants in five unrelated individuals: Individuals 1-4 exhibited developmental and epileptic encephalopathy (DEE) and Individual 5 had intellectual disability and autistic features. CELF2 encodes a nucleocytoplasmic shuttling RNA-binding protein that has multiple roles in RNA processing and is involved in the embryonic development of the central nervous system and heart. Whole-exome sequencing identified the following CELF2 variants: two missense variants [c.1558C>T:p.(Pro520Ser) in unrelated Individuals 1 and 2, and c.1516C>G:p.(Arg506Gly) in Individual 3], one frameshift variant in Individual 4 that removed the last amino acid of CELF2 c.1562dup:p.(Tyr521Ter), possibly resulting in escape from nonsense-mediated mRNA decay (NMD), and one canonical splice site variant, c.272-1G>C in Individual 5, also probably leading to NMD. The identified variants in Individuals 1, 2, 4, and 5 were de novo, while the variant in Individual 3 was inherited from her mosaic mother. Notably, all identified variants, except for c.272-1G>C, were clustered within 20 amino acid residues of the C-terminus, which might be a nuclear localization signal. We demonstrated the extranuclear mislocalization of mutant CELF2 protein in cells transfected with mutant CELF2 complementary DNA plasmids. Our findings indicate that CELF2 variants that disrupt its nuclear localization are associated with DEE.
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Affiliation(s)
- Toshiyuki Itai
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Kazunori Sasaki
- Department of Molecular Biology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Matias Wagner
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Urania Kotzaeridou
- Department of Child Neurology and Metabolic Medicine, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Ines Brösse
- Department of Child Neurology and Metabolic Medicine, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Markus Ries
- Department of Child Neurology and Metabolic Medicine, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Yu Kobayashi
- Department of Child Neurology, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, Niigata, Japan
| | - Jun Tohyama
- Department of Child Neurology, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, Niigata, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Shinagawa-ku, Tokyo, Japan
| | - Winnie P Ong
- Department of Genetics, Kuala Lumpur Hospital, Jalan Pahang, Kuala Lumpur, Malaysia
| | - Hui B Chew
- Department of Genetics, Kuala Lumpur Hospital, Jalan Pahang, Kuala Lumpur, Malaysia
| | - Kavitha Rethanavelu
- Department of Genetics, Kuala Lumpur Hospital, Jalan Pahang, Kuala Lumpur, Malaysia
| | - Emmanuelle Ranza
- Swiss Institute of Genomic Medicine, Medigenome, Geneva, Switzerland
| | - Xavier Blanc
- Swiss Institute of Genomic Medicine, Medigenome, Geneva, Switzerland
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.,Rare Disease Genomics Department, Yokohama City University Hospital, Yokohama, Kanagawa, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.,Rare Disease Genomics Department, Yokohama City University Hospital, Yokohama, Kanagawa, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Yoshiteru Azuma
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Hidehisa Takahashi
- Department of Molecular Biology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Etsuko Miyagi
- Department of Obstetrics and Gynecology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Yoshinori Tsurusaki
- Faculty of Nutritional Science, Sagami Women's University, Sagamihara, Kanagawa, Japan
| | - Hiroshi Doi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Masataka Taguri
- Department of Data Science, Yokohama City University School of Data Science, Yokohama, Kanagawa, Japan
| | - Stylianos E Antonarakis
- Swiss Institute of Genomic Medicine, Medigenome, Geneva, Switzerland.,Department of Genetic Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - Mitsuko Nakashima
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Kanagawa, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
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Quirin K, Hines KA, Wetherill L. Genetic counseling for advanced paternal age: A survey of genetic counselors' current practice. J Genet Couns 2020; 30:428-438. [PMID: 32969081 DOI: 10.1002/jgc4.1328] [Citation(s) in RCA: 4] [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: 04/14/2019] [Revised: 08/09/2020] [Accepted: 08/11/2020] [Indexed: 11/10/2022]
Abstract
Advanced paternal age (APA) has no formal definition, though many publications utilize the cutoff of fathers >40 years of age. The literature demonstrates an association between APA and certain conditions including de novo autosomal dominant disorders, birth defects, and neuropsychiatric conditions. This study surveyed 165 genetic counselors within the National Society of Genetic Counselors to assess their current approach to APA. t Tests, analysis of variance, logistic regression, and chi-squared tests were performed on quantitative data, and content analysis was applied to qualitative data. Although most respondents have discussed APA with a patient (88%), there was no consensus on what age cutoff constitutes APA: >40 (N = 53, 37.9%), >45 (N = 61, 43.6%), >50 (N = 24, 17.1%), or >55 (N = 2, 1.4%). Those who discussed APA were more likely to be prenatal counselors, see more patients per week, be board certified, or be familiar with current APA guidelines. Respondents agreed the literature supports the association of APA with deleterious outcomes (mean agreement = 8.2, median = 8 on a 1 = strongly disagree to 10 = strongly agree). Individuals who discussed APA and were board certified had higher agreement. Content analysis confirmed agreement that the literature supports an association between APA and deleterious outcomes (documented in responses from 31.5% of prenatal respondents, 17.8% others) but noted that available testing and screening options for associated conditions are limited (34.4% of prenatal respondents, 17.4% others). Prenatal and non-prenatal respondents reported similar agreement with the statement that APA is associated with deleterious outcomes. However, most non-prenatal respondents were unfamiliar with current guidelines (80%), and presumably as a result, were also less likely to discuss APA with their patients. Our study identified a need to disseminate information regarding APA and current guidelines to genetic counselors, particularly non-prenatal and those with less experience.
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Affiliation(s)
- Kayla Quirin
- Indiana University School of Medicine Department of Medical and Molecular Genetics, Indianapolis, Indiana, USA.,Washington University School of Medicine Department of Pediatrics Division of Genetics and Genomic Medicine, St. Louis, Missouri, USA
| | - Karrie A Hines
- Division of Maternal Fetal Medicine, Indiana University School of Medicine Department of Obstetrics and Gynecology, Indianapolis, Indiana, USA
| | - Leah Wetherill
- Indiana University School of Medicine Department of Medical and Molecular Genetics, Indianapolis, Indiana, USA
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35
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Zhu L, Lv L, Wu D, Shao J. KAT6B Genetic Variant Identified in a Short Stature Chinese Infant: A Report of Physical Growth in Clinical Spectrum of KAT6B-Related Disorders. Front Pediatr 2020; 8:124. [PMID: 32391291 PMCID: PMC7190791 DOI: 10.3389/fped.2020.00124] [Citation(s) in RCA: 2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 03/06/2020] [Indexed: 02/03/2023] Open
Abstract
Say-Barber-Biesecker-Young-Simpson syndrome (SBBYSS, OMIM#603736) and genitopatellar syndrome (GTPTS, OMIM#606170), characterized by global developmental delay/intellectual disability and special clinical manifestations, are two distinct clinically overlapping syndromes caused by truncating sequence variants in the KAT6B (10q22.2) gene. We detected a de novo heterozygous variant within exon 16 of KAT6B (Chr10p: 76781966-76781967) in a 7-months-old female infant who showed symptoms of short stature, global developmental delay, blepharophimosis, and lacrimal duct anomalies highly consistent with SBBYSS. Following the clinical features, we analyzed the KAT6B gene using Next Generation Sequencing (NGS) techniques. Her parents didn't present the same genetic variant. The patient we reported here is mainly characterized by syndromic forms of short stature and developmental delay, which may contribute to the understanding of clinical genetics for KAT6B-associated disorders.
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Affiliation(s)
- Liuyan Zhu
- Department of Pediatric Health Care, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,National Clinical Research Center for Child Health, Hangzhou, China
| | - Lina Lv
- Department of Pediatric Health Care, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,National Clinical Research Center for Child Health, Hangzhou, China
| | - Dingwen Wu
- National Clinical Research Center for Child Health, Hangzhou, China.,Department of Genetics and Metabolism, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Shao
- Department of Pediatric Health Care, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,National Clinical Research Center for Child Health, Hangzhou, China
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Pacot L, Burin des Roziers C, Laurendeau I, Briand-Suleau A, Coustier A, Mayard T, Tlemsani C, Faivre L, Thomas Q, Rodriguez D, Blesson S, Dollfus H, Muller YG, Parfait B, Vidaud M, Gilbert-Dussardier B, Yardin C, Dauriat B, Derancourt C, Vidaud D, Pasmant E. One NF1 Mutation may Conceal Another. Genes (Basel) 2019; 10:genes10090633. [PMID: 31443423 PMCID: PMC6769760 DOI: 10.3390/genes10090633] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/10/2019] [Accepted: 08/20/2019] [Indexed: 01/01/2023] Open
Abstract
Neurofibromatosis type 1 (NF1) is an autosomal dominant disease with complete penetrance but high variable expressivity. NF1 is caused by loss-of-function mutations in the NF1 gene, a negative regulator of the RAS-MAPK pathway. The NF1 gene has one of the highest mutation rates in human disorders, which may explain the outbreak of independent de novo variants in the same family. Here, we report the co-occurrence of pathogenic variants in the NF1 and SPRED1 genes in six families with NF1 and Legius syndrome, using next-generation sequencing. In five of these families, we observed the co-occurrence of two independent NF1 variants. All NF1 variants were classified as pathogenic, according to the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG-AMP) guidelines. In the sixth family, one sibling inherited a complete deletion of the NF1 gene from her mother and carried a variant of unknown significance in the SPRED1 gene. This variant was also present in her brother, who was diagnosed with Legius syndrome, a differential diagnosis of NF1. This work illustrates the complexity of molecular diagnosis in a not-so-rare genetic disease.
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Affiliation(s)
- Laurence Pacot
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | - Cyril Burin des Roziers
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | - Ingrid Laurendeau
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | - Audrey Briand-Suleau
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | - Audrey Coustier
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
| | - Théodora Mayard
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
| | - Camille Tlemsani
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | - Laurence Faivre
- Inserm, UMR 1231, Génétique des Anomalies du Développement, Université de Bourgogne, 21079 Dijon, France
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d'Enfants, 21079 Dijon, France
| | - Quentin Thomas
- Inserm, UMR 1231, Génétique des Anomalies du Développement, Université de Bourgogne, 21079 Dijon, France
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d'Enfants, 21079 Dijon, France
| | - Diana Rodriguez
- Department of Child Neurology and National Reference Center for Neurogenetic Disorders, Armand Trousseau Hospital, GHUEP, AP-HP, INSERM U1141, 75012 Paris, France
- GRC n°19 ConCer-LD, Sorbonne Université, 75012 Paris, France
| | - Sophie Blesson
- Service de Génétique, CHRU de Tours, 37044 Tours, France
| | - Hélène Dollfus
- Centre de référence pour les Affections Rares en Génétique Ophtalmologique (CARGO), Hôpital Civil, 67091 Strasbourg, France
- Service de Génétique Médicale, Hôpital de Hautepierre, 67200 Strasbourg, France
- Laboratoire de Génétique Médicale, INSERM U1112, 67000 Strasbourg, France
| | | | - Béatrice Parfait
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | - Michel Vidaud
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | | | - Catherine Yardin
- Department of Cytogenetics and clinical genetics, Limoges University Hospital, 87042 Limoges, France
- UMR 7252, Limoges University, CNRS, XLIM, 87000 Limoges, France
| | - Benjamin Dauriat
- Department of Cytogenetics and clinical genetics, Limoges University Hospital, 87042 Limoges, France
| | - Christian Derancourt
- EA 4537, Antilles University, 97261 Fort-de-France, Martinique, France
- DRCI, Martinique University Hospital, 97261 Fort-de-France, Martinique, France
| | - Dominique Vidaud
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France
| | - Eric Pasmant
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, HUPC, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France.
- Institut Cochin, INSERM U1016, Université Paris Descartes, 75014 Paris, France.
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37
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Siggs OM, Russell A, Singh-Grewal D, Wong M, Chan P, Craig ME, O'Loughlin T, Stormon M, Goodnow CC. Preponderance of CTLA4 Variation Associated With Autosomal Dominant Immune Dysregulation in the MYPPPY Motif. Front Immunol 2019; 10:1544. [PMID: 31396201 PMCID: PMC6664875 DOI: 10.3389/fimmu.2019.01544] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 03/14/2019] [Accepted: 06/20/2019] [Indexed: 01/05/2023] Open
Abstract
One of the primary targets of immune checkpoint inhibition is the negative immune regulatory molecule CTLA-4. Immune-related adverse events are commonly observed following CTLA-4 inhibition in melanoma treatment, and a spectrum of these conditions are also observed in individuals with germline haploinsufficiency of CTLA4. Here we describe a heterozygous de novo missense variant of CTLA4 in a young girl with childhood-onset autoimmune hepatitis and polyarthritis, the latter responding to treatment with CTLA-4-Ig fusion protein. This variant lay within the highly conserved MYPPPY motif of CTLA-4: a critical structural determinant of ligand binding, which is also bound by the anti-CTLA-4 monoclonal antibody ipilimumab. Within the spectrum of CTLA4 variants reported, missense variants in the MYPPPY motif were overrepresented when compared to variants within a control population, highlighting the physiological importance of this motif in both the genetic and pharmacological regulation of autoimmunity and anti-tumor immunity.
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Affiliation(s)
- Owen M Siggs
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Department of Ophthalmology, Flinders University, Adelaide, SA, Australia
| | - Amanda Russell
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Davinder Singh-Grewal
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Melanie Wong
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Pearl Chan
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Maria E Craig
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Ted O'Loughlin
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Michael Stormon
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Christopher C Goodnow
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, The University of New South Wales, Sydney, NSW, Australia
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38
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Siggs OM, Russell A, Singh-Grewal D, Wong M, Chan P, Craig ME, O'Loughlin T, Stormon M, Goodnow CC. Preponderance of CTLA4 Variation Associated With Autosomal Dominant Immune Dysregulation in the MYPPPY Motif. Front Immunol 2019. [PMID: 31396201 DOI: 10.3389/fimmu.2019.01544/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
One of the primary targets of immune checkpoint inhibition is the negative immune regulatory molecule CTLA-4. Immune-related adverse events are commonly observed following CTLA-4 inhibition in melanoma treatment, and a spectrum of these conditions are also observed in individuals with germline haploinsufficiency of CTLA4. Here we describe a heterozygous de novo missense variant of CTLA4 in a young girl with childhood-onset autoimmune hepatitis and polyarthritis, the latter responding to treatment with CTLA-4-Ig fusion protein. This variant lay within the highly conserved MYPPPY motif of CTLA-4: a critical structural determinant of ligand binding, which is also bound by the anti-CTLA-4 monoclonal antibody ipilimumab. Within the spectrum of CTLA4 variants reported, missense variants in the MYPPPY motif were overrepresented when compared to variants within a control population, highlighting the physiological importance of this motif in both the genetic and pharmacological regulation of autoimmunity and anti-tumor immunity.
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Affiliation(s)
- Owen M Siggs
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Department of Ophthalmology, Flinders University, Adelaide, SA, Australia
| | - Amanda Russell
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Davinder Singh-Grewal
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Melanie Wong
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Pearl Chan
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Maria E Craig
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Ted O'Loughlin
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Michael Stormon
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Christopher C Goodnow
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, The University of New South Wales, Sydney, NSW, Australia
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39
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Pranckėnienė L, Preikšaitienė E, Gueneau L, Reymond A, Kučinskas V. De Novo Duplication in the CHD7 Gene Associated With Severe CHARGE Syndrome. Genomics Insights 2019; 12:1178631019839010. [PMID: 31043788 PMCID: PMC6446253 DOI: 10.1177/1178631019839010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 02/28/2019] [Indexed: 01/14/2023]
Abstract
CHARGE syndrome is an autosomal dominant developmental disorder associated with a constellation of traits involving almost every organ and sensory system, in particular congenital anomalies, including choanal atresia and malformations of the heart, inner ear, and retina. Variants in CHD7 have been shown to cause CHARGE syndrome. Here, we report the identification of a novel de novo p.Asp2119_Pro2120ins6 duplication variant in a conserved region of CHD7 in a severely affected boy presenting with 3 and 5 of the CHARGE cardinal major and minor signs, respectively, combined with congenital umbilical hernia, congenital hernia at the linea alba, mildly hypoplastic inferior vermis, slight dilatation of the lateral ventricles, prominent metopic ridge, and hypoglycemic episodes.
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Affiliation(s)
- Laura Pranckėnienė
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Eglė Preikšaitienė
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
| | - Lucie Gueneau
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Vaidutis Kučinskas
- Department of Human and Medical Genetics, Faculty of Medicine, Institute of Biomedical Sciences, Vilnius University, Vilnius, Lithuania
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40
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Cai XB, Wu KC, Zhang X, Lv JN, Jin GH, Xiang L, Chen J, Huang XF, Pan D, Lu B, Lu F, Qu J, Jin ZB. Whole-exome sequencing identified ARL2 as a novel candidate gene for MRCS (microcornea, rod-cone dystrophy, cataract, and posterior staphyloma) syndrome. Clin Genet 2019; 96:61-71. [PMID: 30945270 DOI: 10.1111/cge.13541] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 03/20/2019] [Accepted: 03/21/2019] [Indexed: 01/01/2023]
Abstract
Adenosine diphosphate (ADP)-ribosylation factor-like 2 (ARL2) protein participates in a broad range of cellular processes and acts as a mediator for mutant ARL2BP in cilium-associated retinitis pigmentosa and for mutant HRG4 in mitochondria-related photoreceptor degeneration. However, mutant ARL2 has not been linked to any human disease so far. Here, we identified a de novo variant in ARL2 (c.44G > T, p.R15L) in a Chinese pedigree with MRCS (microcornea, rod-cone dystrophy, cataract, and posterior staphyloma) syndrome through whole-exome sequencing and co-segregation analysis. Co-immunoprecipitation assay and immunoblotting confirmed that the mutant ARL2 protein showed a 62% lower binding affinity for HRG4 while a merely 18% lower binding affinity for ARL2BP. Immunofluorescence images of ARL2 and HRG4 co-localizing with cytochrome c in HeLa cells described their relationship with mitochondria. Further analyses of the mitochondrial respiratory chain and adenosine triphosphate production showed significant abnormalities under an ARL2-mutant condition. Finally, we generated transgenic mice to test the pathogenicity of this variant and observed retinal degeneration complicated with microcornea and cataract that were similar to those in our patients. In conclusion, we uncover ARL2 as a novel candidate gene for MRCS syndrome and suggest a mitochondria-related mechanism of the first ARL2 variant through site-directed mutagenesis studies.
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Affiliation(s)
- Xue-Bi Cai
- Lab for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research; Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou Medical University, Wenzhou, China
| | - Kun-Chao Wu
- Lab for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research; Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou Medical University, Wenzhou, China
| | - Xiao Zhang
- Lab for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research; Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou Medical University, Wenzhou, China
| | - Ji-Neng Lv
- Lab for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research; Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou Medical University, Wenzhou, China
| | - Guang-Hui Jin
- Lab for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research; Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou Medical University, Wenzhou, China
| | - Lue Xiang
- Lab for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research; Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou Medical University, Wenzhou, China
| | - Jie Chen
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou Medical University, Wenzhou, China
| | - Xiu-Feng Huang
- Lab for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research; Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou Medical University, Wenzhou, China
| | - Deng Pan
- Lab for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research; Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou Medical University, Wenzhou, China
| | - Bin Lu
- Protein Quality Control and Diseases Laboratory, Institute of Biophysics, School of Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Fan Lu
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou Medical University, Wenzhou, China
| | - Jia Qu
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou Medical University, Wenzhou, China
| | - Zi-Bing Jin
- Lab for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research; Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Vision Science, Wenzhou Medical University, Wenzhou, China
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41
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Song C, Li N, Hu X, Shi Y, Chen L, Zhou T, Xu X, Shen J, Zhu M. A de novo variant in MMP13 identified in a patient with dominant metaphyseal anadysplasia. Eur J Med Genet 2018; 62:103575. [PMID: 30439533 DOI: 10.1016/j.ejmg.2018.11.009] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 10/05/2018] [Accepted: 11/09/2018] [Indexed: 01/26/2023]
Abstract
Metaphyseal anadysplasia 1 (MIM# 602111) belongs to a heterogeneous group of skeletal diseases characterized by an autosomal dominant form of growth defects due to metaphyseal changes with epiphyseal involvement similar to other metaphyseal disorders. Matrix metalloproteinase 13 encoded by MMP13 presumably plays important roles in bone formation and growth, and pathogenic variants in MMP13 have been identified to cause metaphyseal anadysplasia 1. Only six pathogenic variants in MMP13 have been previously reported worldwide. The genotype-phenotype correlation of MMP13-related disorders has not been fully understood. Here we reported the identification of a previously unreported pathogenic heterozygous de novo variant NM_002427.3:c.212T > C/p.Met71Thr in MMP13 in a Chinese male pediatric patient with metaphyseal anadysplasia 1 and additional phenotypes, including mild rickets-like changes observed on upper long bone metaphyses and patchy bone defects on the spine vertebrae particularly resolved by childhood. Our findings not only expand genotype and phenotype spectrums of MMP13-related disorders but also offer further information for precise diagnosis and classification of metaphyseal anadysplasia disorders.
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Affiliation(s)
- Cui Song
- Department of Endocrinology and Genetic Metabolic Diseases, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, 400014, Chongqing, China
| | - Niu Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, 200127, Shanghai, China
| | - Xuyun Hu
- Center for Medical Genetics, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, 100045, Beijing, China
| | - Yu Shi
- Department of Clinical Laboratory, Children's Hospital of Chongqing Medical University, 400014, Chongqing, China
| | - Lili Chen
- Department of Endocrinology and Genetic Metabolic Diseases, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, 400014, Chongqing, China
| | - Ting Zhou
- Department of Endocrinology and Genetic Metabolic Diseases, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, 400014, Chongqing, China
| | - Xuejiao Xu
- Department of Endocrinology and Genetic Metabolic Diseases, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, 400014, Chongqing, China
| | - Jun Shen
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.
| | - Min Zhu
- Department of Endocrinology and Genetic Metabolic Diseases, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, 400014, Chongqing, China.
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42
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He N, Lin ZJ, Wang J, Wei F, Meng H, Liu XR, Chen Q, Su T, Shi YW, Yi YH, Liao WP. Evaluating the pathogenic potential of genes with de novo variants in epileptic encephalopathies. Genet Med 2019; 21:17-27. [PMID: 29895856 DOI: 10.1038/s41436-018-0011-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 03/20/2018] [Indexed: 01/08/2023] Open
Abstract
Epileptic encephalopathies comprise a group of catastrophic epilepsies with heterogeneous genetic etiology. Although next-generation sequencing techniques can reveal a number of de novo variants in epileptic encephalopathies, evaluating the pathogenicity of these variants can be challenging. Determining the pathogenic potential of genes in epileptic encephalopathies is critical before evaluating the pathogenicity of variants identified in an individual. We reviewed de novo variants in epileptic encephalopathies, including their genotypes and functional consequences. We then evaluated the pathogenic potential of genes, with the following additional considerations: (1) recurrence of variants in unrelated cases, (2) information of previously defined phenotypes, and (3) data from genetic experimental studies. Genes related to epileptic encephalopathy revealed pathogenicity with distinct functional alterations, i.e., either a gain of function or loss of function in the majority; however, several genes warranted further study to confirm their pathogenic potential. Whether a gene was associated with distinct phenotype, the genotype (or functional alteration)-–phenotype correlation, and quantitative correlation between genetic impairment and phenotype severity were suggested to be specific evidence in determining the pathogenic role of genes. Data from epileptic encephalopathy-related genes would be helpful in outlining guidelines for evaluating the pathogenic potential of genes in other genetic disorders.
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43
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Carvill GL, Liu A, Mandelstam S, Schneider A, Lacroix A, Zemel M, McMahon JM, Bello-Espinosa L, Mackay M, Wallace G, Waak M, Zhang J, Yang X, Malone S, Zhang YH, Mefford HC, Scheffer IE. Severe infantile onset developmental and epileptic encephalopathy caused by mutations in autophagy gene WDR45. Epilepsia 2017; 59:e5-e13. [PMID: 29171013 DOI: 10.1111/epi.13957] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2017] [Indexed: 01/08/2023]
Abstract
Heterozygous de novo variants in the autophagy gene, WDR45, are found in beta-propeller protein-associated neurodegeneration (BPAN). BPAN is characterized by adolescent onset dementia and dystonia; 66% patients have seizures. We asked whether WDR45 was associated with developmental and epileptic encephalopathy (DEE). We performed next generation sequencing of WDR45 in 655 patients with developmental and epileptic encephalopathies. We identified 3/655 patients with DEE plus 4 additional patients with de novo WDR45 pathogenic variants (6 truncations, 1 missense); all were female. Six presented with DEE and 1 with early onset focal seizures and profound regression. Median seizure onset was 12 months, 6 had multiple seizure types, and 5/7 had focal seizures. Three patients had magnetic resonance susceptibility-weighted imaging; blooming was noted in the globus pallidi and substantia nigra in the 2 older children aged 4 and 9 years, consistent with iron accumulation. We show that de novo pathogenic variants are associated with a range of developmental and epileptic encephalopathies with profound developmental consequences.
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Affiliation(s)
- Gemma L Carvill
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Aijie Liu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Simone Mandelstam
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia.,Departments of Paediatrics and Radiology, University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Amy Schneider
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, Victoria, Australia
| | - Amy Lacroix
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Matthew Zemel
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Jacinta M McMahon
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, Victoria, Australia
| | - Luis Bello-Espinosa
- Department of Paediatrics, University of Calgary, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Mark Mackay
- Departments of Paediatrics and Radiology, University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Geoffrey Wallace
- Department of Neurology, Lady Cilento Children's Hospital, Brisbane, Queensland, Australia
| | - Michaela Waak
- Department of Neurology, Lady Cilento Children's Hospital, Brisbane, Queensland, Australia
| | - Jing Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xiaoling Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Stephen Malone
- Department of Neurology, Lady Cilento Children's Hospital, Brisbane, Queensland, Australia
| | - Yue-Hua Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Ingrid E Scheffer
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia.,Departments of Paediatrics and Radiology, University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia.,Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Victoria, Australia
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Harel T, Yoon WH, Garone C, Gu S, Coban-Akdemir Z, Eldomery MK, Posey JE, Jhangiani SN, Rosenfeld JA, Cho MT, Fox S, Withers M, Brooks SM, Chiang T, Duraine L, Erdin S, Yuan B, Shao Y, Moussallem E, Lamperti C, Donati MA, Smith JD, McLaughlin HM, Eng CM, Walkiewicz M, Xia F, Pippucci T, Magini P, Seri M, Zeviani M, Hirano M, Hunter JV, Srour M, Zanigni S, Lewis RA, Muzny DM, Lotze TE, Boerwinkle E, Gibbs RA, Hickey SE, Graham BH, Yang Y, Buhas D, Martin DM, Potocki L, Graziano C, Bellen HJ, Lupski JR, Bellen HJ, Lupski JR. Recurrent De Novo and Biallelic Variation of ATAD3A, Encoding a Mitochondrial Membrane Protein, Results in Distinct Neurological Syndromes. Am J Hum Genet 2016; 99:831-845. [PMID: 27640307 DOI: 10.1016/j.ajhg.2016.08.007] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [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: 06/06/2016] [Accepted: 08/04/2016] [Indexed: 12/22/2022] Open
Abstract
ATPase family AAA-domain containing protein 3A (ATAD3A) is a nuclear-encoded mitochondrial membrane protein implicated in mitochondrial dynamics, nucleoid organization, protein translation, cell growth, and cholesterol metabolism. We identified a recurrent de novo ATAD3A c.1582C>T (p.Arg528Trp) variant by whole-exome sequencing (WES) in five unrelated individuals with a core phenotype of global developmental delay, hypotonia, optic atrophy, axonal neuropathy, and hypertrophic cardiomyopathy. We also describe two families with biallelic variants in ATAD3A, including a homozygous variant in two siblings, and biallelic ATAD3A deletions mediated by nonallelic homologous recombination (NAHR) between ATAD3A and gene family members ATAD3B and ATAD3C. Tissue-specific overexpression of borR534W, the Drosophila mutation homologous to the human c.1582C>T (p.Arg528Trp) variant, resulted in a dramatic decrease in mitochondrial content, aberrant mitochondrial morphology, and increased autophagy. Homozygous null bor larvae showed a significant decrease of mitochondria, while overexpression of borWT resulted in larger, elongated mitochondria. Finally, fibroblasts of an affected individual exhibited increased mitophagy. We conclude that the p.Arg528Trp variant functions through a dominant-negative mechanism that results in small mitochondria that trigger mitophagy, resulting in a reduction in mitochondrial content. ATAD3A variation represents an additional link between mitochondrial dynamics and recognizable neurological syndromes, as seen with MFN2, OPA1, DNM1L, and STAT2 mutations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
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45
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Abstract
Spontaneously arising (de novo) genetic variants are important in human disease, yet every individual carries many such variants, with a median of 1 de novo variant affecting the protein-coding portion of the genome. A recently described mutational model provides a powerful framework for the robust statistical evaluation of such coding variants, enabling the interpretation of de novo variation in human disease. Here we describe a new open-source software package, denovolyzeR, that implements this model and provides tools for the analysis of de novo coding sequence variants.
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Affiliation(s)
- James S Ware
- Department of Genetics, Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Analytical and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.,NIHR Cardiovascular Biomedical Research Unit at Royal Brompton Hospital and Imperial College London, London, United Kingdom
| | - Kaitlin E Samocha
- Department of Genetics, Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Analytical and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jason Homsy
- Department of Genetics, Harvard Medical School, Boston, Massachusetts.,Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Mark J Daly
- Department of Genetics, Harvard Medical School, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Analytical and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
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