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Wei S, Zhang M, Li Y, Yang W, Zhang C, Liu F, Chen S, Ban B, He D. Identification and functional analysis of first heterozygous frameshift mutation in the GHRH gene in a Chinese boy with isolated growth hormone deficiency. Gene 2024; 907:148283. [PMID: 38354915 DOI: 10.1016/j.gene.2024.148283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/26/2024] [Accepted: 02/09/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND Isolated growth hormone deficiency (IGHD) is a rare genetically heterogeneous disorder caused primarily by mutations in GH1 and GH releasing hormone receptor (GHRHR). The aim of this study was to identify the molecular etiology of a Chinese boy with IGHD. METHODS Whole-exome sequencing, sanger sequencing and bioinformatic analysis were performed to screen for candidate mutations. The impacts of candidate mutation on gene expression, intracellular localization and protein function were further evaluated by in vitro assays. RESULTS A novel heterozygous frameshift mutation in the GHRH gene (c.91dupC, p.R31Pfs*98) was identified in a Chinese boy clinically diagnosed as having IGHD. The mutation was absent in multiple public databases, and considered as deleterious using in silico prediction, conservative analysis and three-dimensional homology modeling. Furthermore, mRNA and protein expression levels of mutant GHRH were significantly increased than wild-type GHRH (p < 0.05). Moreover, mutant GHRH showed an aberrant accumulation within the cytoplasm, and obviously reduced ability to stimulate GH secretion and cAMP accumulation in human GHRHR-expressing pituitary GH3 cells compared to wild-type GHRH (p < 0.05). CONCLUSION Our study discovered the first loss-of function mutation of GHRH in a Chinese boy with IGHD and provided new insights on IGHD pathogenesis caused by GHRH haploinsufficiency.
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Affiliation(s)
- Shuoshuo Wei
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, PR China; Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, PR China
| | - Mei Zhang
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, PR China; Chinese Research Center for Behavior Medicine in Growth and Development, Jining, PR China
| | - Yanying Li
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, PR China; Chinese Research Center for Behavior Medicine in Growth and Development, Jining, PR China
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, PR China
| | - Chuanpeng Zhang
- Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, PR China
| | - Fupeng Liu
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, PR China; Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, PR China
| | - Shuxiong Chen
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, PR China; Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, PR China
| | - Bo Ban
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, PR China; Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, PR China; Chinese Research Center for Behavior Medicine in Growth and Development, Jining, PR China.
| | - Dongye He
- Department of Endocrinology, Genetics and Metabolism, Affiliated Hospital of Jining Medical University, Jining, PR China; Medical Research Center, Affiliated Hospital of Jining Medical University, Jining, PR China.
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Li Q, Chen Z, Wang J, Xu K, Fan X, Gong C, Wu Z, Zhang TJ, Wu N. Molecular Diagnostic Yield of Exome Sequencing and Chromosomal Microarray in Short Stature: A Systematic Review and Meta-Analysis. JAMA Pediatr 2023; 177:1149-1157. [PMID: 37695591 PMCID: PMC10495925 DOI: 10.1001/jamapediatrics.2023.3566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/21/2023] [Indexed: 09/12/2023]
Abstract
Importance Currently, the diagnostic yield of exome sequencing (ES) and chromosomal microarray analysis (CMA) for short stature cohorts is uncertain. Despite previous studies reporting the widespread use of ES and CMA, a definitive diagnostic yield has not been established. Objective To investigate the diagnostic yield of ES and CMA in short stature. Data Sources A systematic literature search was conducted using relevant keywords in 3 databases (PubMed, Embase, and Web of Science) in February 2023. Study Selection Eligible studies for meta-analysis were those that had at least 10 participants with short stature who were diagnosed using either ES or CMA and the number of diagnosed patients was reported. Of 5222 identified studies, 20 were eventually included in the study. Data Extraction and Synthesis Two independent investigators extracted relevant information from each study, which was then synthesized using proportional meta-analysis to obtain the overall diagnostic yield of ES and CMA. Main Outcomes and Measures The primary outcome measure was to determine the overall diagnostic yield of ES and CMA. A subgroup meta-analysis was also performed to assess if the diagnostic yield varied depending on whether ES was used as a first-tier or last-resort test. Additionally, a meta-regression was carried out to investigate how the diagnostic yield varied over time. Results Twenty studies were included, comprising 1350 patients with short stature who underwent ES and 1070 patients who completed CMA. The overall diagnostic yield of ES among the cohorts and CMA among the cohorts was found to be 27.1% (95% CI, 18.1%-37.2%) and 13.6% (95% CI, 9.2%-18.7%), respectively. No statistically significant difference was observed between the first-tier (27.8%; 95% CI, 15.7%-41.8%) and last-resort groups (25.6%; 95% CI, 13.6%-39.6%) (P = .83) or in the percentage of positively diagnosed patients over time. No statistically significant difference was observed between the first-tier (27.8%; 95% CI, 15.7%-41.8%) and last-resort groups (25.6%; 95% CI, 13.6%-39.6%) (P = .83) or in the percentage of positively diagnosed patients over time. Conclusion and Relevance This systematic review and meta-analysis provides high-level evidence supporting the diagnostic efficacy of ES and CMA in patients with short stature. The findings serve as a solid reference for clinicians when making informed decisions about recommending these genetic tests.
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Affiliation(s)
- Qing Li
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences; Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity; Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences; Beijing, China
| | - Zefu Chen
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences; Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity; Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences; Beijing, China
- Division of Spine Surgery, Department of Orthopedics, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jie Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences; Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity; Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences; Beijing, China
| | - Kexin Xu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences; Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity; Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences; Beijing, China
| | - Xin Fan
- Department of Pediatric, The second affiliated hospital of Guangxi Medical University, Guangxi, China
| | - Chunxiu Gong
- Department of Endocrinology, Genetics and Metabolism, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Zhihong Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences; Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity; Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences; Beijing, China
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences; Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity; Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences; Beijing, China
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences; Beijing, 100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity; Beijing, China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences; Beijing, China
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Ahmad S, Ali MZ, Abbasi SW, Abbas S, Ahmed I, Abbas S, Nawaz S, Ziab M, Ahmed I, Fakhro KA, Khan MA, Akil AAS. A GHRHR founder mutation causes isolated growth hormone deficiency type IV in a consanguineous Pakistani family. Front Endocrinol (Lausanne) 2023; 14:1066182. [PMID: 36960394 PMCID: PMC10029353 DOI: 10.3389/fendo.2023.1066182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/23/2023] [Indexed: 03/09/2023] Open
Abstract
Background Isolated growth hormone deficiency (IGHD) is caused by a severe shortage or absence of growth hormone (GH), which results in aberrant growth and development. Patients with IGHD type IV (IGHD4) have a short stature, reduced serum GH levels, and delayed bone age. Objectives To identify the causative mutation of IGHD in a consanguineous family comprising four affected patients with IGHD4 (MIM#618157) and explore its functional impact in silico. Methods Clinical and radiological studies were performed to determine the phenotypic spectrum and hormonal profile of the disease, while whole-exome sequencing (WES) and Sanger sequencing were performed to identify the disease-causing mutation. In-silico studies involved protein structural modeling and docking, and molecular dynamic simulation analyses using computational tools. Finally, data from the Qatar Genome Program (QGP) were screened for the presence of the founder variant in the Qatari population. Results All affected individuals presented with a short stature without gross skeletal anomalies and significantly reduced serum GH levels. Genetic mapping revealed a homozygous nonsense mutation [NM_000823:c.G214T:p.(Glu72*)] in the third exon of the growth-hormone-releasing hormone receptor gene GHRHR (MIM#139191) that was segregated in all patients. The substituted amber codon (UAG) seems to truncate the protein by deleting the C-terminus GPCR domain, thus markedly disturbing the GHRHR receptor and its interaction with the growth hormone-releasing hormone. Conclusion These data support that a p.Glu72* founder mutation in GHRHR perturbs growth hormone signaling and causes IGHD type IV. In-silico and biochemical analyses support the pathogenic effect of this nonsense mutation, while our comprehensive phenotype and hormonal profiling has established the genotype-phenotype correlation. Based on the current study, early detection of GHRHR may help in better therapeutic intervention.
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Affiliation(s)
- Safeer Ahmad
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Zeeshan Ali
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Khyber Pakhtunkhwa, Pakistan
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Punjab, Pakistan
| | - Safdar Abbas
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Khyber Pakhtunkhwa, Pakistan
| | - Iftikhar Ahmed
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Khyber Pakhtunkhwa, Pakistan
| | - Shakil Abbas
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Khyber Pakhtunkhwa, Pakistan
| | - Shoaib Nawaz
- Laboratory of Genomic Medicine-Precision Medicine Program, Sidra Medicine, Doha, Qatar
| | - Mubarak Ziab
- Department of Human Genetics, Precision Medicine of Diabetes Prevention Program, Sidra Medicine, Doha, Qatar
| | - Ikhlak Ahmed
- Department of Human Genetics, Precision Medicine of Diabetes Prevention Program, Sidra Medicine, Doha, Qatar
| | - Khalid A. Fakhro
- Laboratory of Genomic Medicine-Precision Medicine Program, Sidra Medicine, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medical College-Doha, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Muzammil Ahmad Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, D.I. Khan, Khyber Pakhtunkhwa, Pakistan
| | - Ammira Al-Shabeeb Akil
- Laboratory of Genomic Medicine-Precision Medicine Program, Sidra Medicine, Doha, Qatar
- Department of Human Genetics, Precision Medicine of Diabetes Prevention Program, Sidra Medicine, Doha, Qatar
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Shi M, Liang Y, Xie B, Wei X, Zheng H, Gui C, Huang R, Fan X, Li C, Wei X, Ma Y, Chen S, Chen Y, Gui B. Case report: A novel heterozygous synonymous variant in deep exon region of NIPBL gene generating a non-canonical splice donor in a patient with cornelia de lange syndrome. Front Genet 2022; 13:1056127. [PMID: 36506332 PMCID: PMC9726764 DOI: 10.3389/fgene.2022.1056127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/11/2022] [Indexed: 11/24/2022] Open
Abstract
Cornelia de Lange syndrome (CdLS) is an autosomal dominant or X-linked genetic disease with significant genetic heterogeneity. Variants of the NIPBL gene are responsible for CdLS in 60% of patients. Herein, we report the case of a patient with CdLS showing distinctive facial features, microcephaly, developmental delay, and growth retardation. Whole exome sequencing was performed for the patient, and a novel de novo heterozygous synonymous variant was identified in the deep region of exon 40 in the NIPBL gene (NM_133433.4: c. 6819G > T, p. Gly2273 = ). The clinical significance of the variant was uncertain according to the ACMG/AMP guidelines; however, based on in silico analysis, it was predicted to alter mRNA splicing. To validate the prediction, a reverse transcriptase-polymerase chain reaction was conducted. The variant activated a cryptic splice donor, generating a short transcript of NIPBL. A loss of 137 bp at the 3' end of NIPBL exon 40 was detected, which potentially altered the open reading frame by inserting multiple premature termination codons. Quantitative real-time PCR analysis showed that the ratio of the transcription level of the full-length transcript to that of the altered short transcript in the patient was 5:1, instead of 1:1. These findings may explain the relatively mild phenotype of the patient, regardless of the loss of function of the truncated protein due to a frameshift in the mRNA. To the best of our knowledge, this study is the first to report a synonymous variant in the deep exon regions of the NIPBL gene responsible for CdLS. The identified variant expands the mutational spectrum of the NIPBL gene. Furthermore, synonymous variations may be pathogenic, which should not be ignored in the clinical and genetic diagnosis of the disease.
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Affiliation(s)
- Meizhen Shi
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yuying Liang
- Department of Pediatrics, The Traditional Chinese Medicine Hospital of YuLin, Yulin, China
| | - Bobo Xie
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xianda Wei
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Haiyang Zheng
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chunrong Gui
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Rong Huang
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xin Fan
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chuan Li
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiaojiao Wei
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yunting Ma
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Shaoke Chen
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,*Correspondence: Shaoke Chen, ; Yujun Chen, ; Baoheng Gui,
| | - Yujun Chen
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,*Correspondence: Shaoke Chen, ; Yujun Chen, ; Baoheng Gui,
| | - Baoheng Gui
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,*Correspondence: Shaoke Chen, ; Yujun Chen, ; Baoheng Gui,
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Castets S, Villanueva C, Vergier J, Brue T, Saveanu A, Reynaud R. Clinical, radiological, and molecular diagnosis of congenital pituitary diseases causing short stature. Arch Pediatr 2022; 28:8S33-8S38. [PMID: 37870532 DOI: 10.1016/s0929-693x(22)00041-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Short stature in children can be caused by congenital pituitary disorders involving at least one form of growth hormone deficiency. Clinical and radiological evaluations of the index case and family history assessments are essential to guide genetic diagnostic testing and interpret results. The first-line approach is panel testing of genes involved in pituitary development with variants known to be pathogenic in this context. It identifies a genetic cause in less than 10% of cases, however. Whole-exome and whole-genome sequencing techniques may provide original information but also raise new questions regarding the pathophysiological role of identified variants. These new tools can make genetic counselling more complex. The role of clinicians in these interpretations is therefore important. © 2022 French Society of Pediatrics. Published by Elsevier Masson SAS. All rights reserved.
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Affiliation(s)
- S Castets
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Hôpital Timone Enfants, Service de Pédiatrie Multidisciplinaire, Marseille, France; Centre de Référence des Maladies Rares de l'Hypophyse HYPO, Marseille, France.
| | - C Villanueva
- Hospices Civils de Lyon (HCL), Hôpital Femme Mère Enfant (HFME), Service d'Endocrinologie pédiatrique, Bron, France; Centre de Référence des Maladies Rares de l'Hypophyse HYPO, Marseille, France
| | - J Vergier
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Hôpital Timone Enfants, Service de Pédiatrie Multidisciplinaire, Marseille, France; Centre de Référence des Maladies Rares de l'Hypophyse HYPO, Marseille, France
| | - T Brue
- Hospices Civils de Lyon (HCL), Hôpital Femme Mère Enfant (HFME), Service d'Endocrinologie pédiatrique, Bron, France; Centre de Référence des Maladies Rares de l'Hypophyse HYPO, Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), Service d'Endocrinologie, Hôpital de la Conception, Marseille, France; Institut Marseille Maladies Rares (MarMaRa), Marseille, France
| | - A Saveanu
- Centre de Référence des Maladies Rares de l'Hypophyse HYPO, Marseille, France; Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale (INSERM), Marseille Medical Genetics (MMG), U 1251, Marseille, France; Institut Marseille Maladies Rares (MarMaRa), Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), Laboratoire de Biologie Moléculaire, Hôpital de la Conception, Marseille, France
| | - R Reynaud
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Hôpital Timone Enfants, Service de Pédiatrie Multidisciplinaire, Marseille, France; Centre de Référence des Maladies Rares de l'Hypophyse HYPO, Marseille, France; Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale (INSERM), Marseille Medical Genetics (MMG), U 1251, Marseille, France; Institut Marseille Maladies Rares (MarMaRa), Marseille, France
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