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Liu L, Li J, Li J, Hu H, Liu J, Tang P. Novel heterozygous mutation in the SHOX gene leading to familial idiopathic short stature: A case report and literature review. Medicine (Baltimore) 2023; 102:e35471. [PMID: 37832088 PMCID: PMC10578768 DOI: 10.1097/md.0000000000035471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND The pathogenic mutation of short stature homeobox (SHOX) gene is one of the main genetic causes of short stature in children, with an incidence rate of 1/1000~1/2000 and the main clinical manifestations are short stature and (or) limb skeletal abnormalities. SHOX gene mutations are mostly large deletions of regulatory sequence genes, while exon mutations are relatively rare. The pathogenic rate of mutations occurring in exon 5 is only 1/50 000~1/100 000. This study reviewed the clinical data of a child with SHOX gene mutation in exon 5, and analyzed the clinical phenotype, pathogenesis, diagnosis, treatment and prognosis of SHOX gene mutation in combination with relevant literature at home and abroad. CASE PRESENTATION The patient was an 8-year-old girl with a height of 105.2 cm (-4.31 standard deviations). Her sitting height/height ratio was 56.8% (>55.5%), and she exhibited high-arched palate, irregular dentition, micrognathia, short fingers, and a normal growth hormone stimulation test. Whole-exome sequencing was performed, and Sanger sequencing was used for site validation. The sequencing results revealed a heterozygous mutation of c.577G > A in exon 5 of the SHOX gene, inherited from the father. The clinical symptoms of the proband were consistent with the phenotype of short stature idiopathic familial associated with SHOX gene mutations. The father, grandfather, uncle, and sister of the proband all had the c.577G > A heterozygous mutation. Therefore, the clinical diagnosis was childhood short stature caused by SHOX gene defects. The SHOX: c.577G > A mutation is likely to be the genetic etiology of familial idiopathic short stature in this family, and this novel mutation enriches the mutation spectrum of the SHOX gene. CONCLUSION This is the first case report of familial idiopathic dwarfism caused by mutation at the c.577G > A locus of exon 5 of SHOX gene in the world. This novel mutation enriches the mutation spectrum of the SHOX gene. It is important to emphasize genetic testing, including the SHOX gene, in patients with familial idiopathic short stature and to provide timely growth hormone therapy to individuals with short stature caused by SHOX gene mutations in order to improve their adult height.
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Affiliation(s)
- Lifang Liu
- Lishui Maternal and Child Health Hospital, Lishui, Zhejiang, China
| | - Junsheng Li
- Lishui Maternal and Child Health Hospital, Lishui, Zhejiang, China
| | - Jiarui Li
- Department of Orthopaedic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hui Hu
- Lishui Maternal and Child Health Hospital, Lishui, Zhejiang, China
| | - Jiao Liu
- Lishui Maternal and Child Health Hospital, Lishui, Zhejiang, China
| | - Ping Tang
- Jiaxing Maternity and Children Health Care Hospital/The Affiliated Women and Children’s Hospital of Jiaxing University, Jiaxing, Zhejiang, China
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2
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Delea M, Massara LS, Espeche LD, Bidondo MP, Barbero P, Oliveri J, Brun P, Fabro M, Galain M, Fernández CS, Taboas M, Bruque CD, Kolomenski JE, Izquierdo A, Berenstein A, Cosentino V, Martinoli C, Vilas M, Rittler M, Mendez R, Furforo L, Liascovich R, Groisman B, Rozental S, Dain L. Genetic Analysis Algorithm for the Study of Patients with Multiple Congenital Anomalies and Isolated Congenital Heart Disease. Genes (Basel) 2022; 13:1172. [PMID: 35885957 PMCID: PMC9317700 DOI: 10.3390/genes13071172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/16/2022] [Accepted: 06/27/2022] [Indexed: 11/20/2022] Open
Abstract
Congenital anomalies (CA) affect 3-5% of newborns, representing the second-leading cause of infant mortality in Argentina. Multiple congenital anomalies (MCA) have a prevalence of 2.26/1000 births in newborns, while congenital heart diseases (CHD) are the most frequent CA with a prevalence of 4.06/1000 births. The aim of this study was to identify the genetic causes in Argentinian patients with MCA and isolated CHD. We recruited 366 patients (172 with MCA and 194 with isolated CHD) born between June 2015 and August 2019 at public hospitals. DNA from peripheral blood was obtained from all patients, while karyotyping was performed in patients with MCA. Samples from patients presenting conotruncal CHD or DiGeorge phenotype (n = 137) were studied using MLPA. Ninety-three samples were studied by array-CGH and 18 by targeted or exome next-generation sequencing (NGS). A total of 240 patients were successfully studied using at least one technique. Cytogenetic abnormalities were observed in 13 patients, while 18 had clinically relevant imbalances detected by array-CGH. After MLPA, 26 patients presented 22q11 deletions or duplications and one presented a TBX1 gene deletion. Following NGS analysis, 12 patients presented pathogenic or likely pathogenic genetic variants, five of them, found in KAT6B, SHH, MYH11, MYH7 and EP300 genes, are novel. Using an algorithm that combines molecular techniques with clinical and genetic assessment, we determined the genetic contribution in 27.5% of the analyzed patients.
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Affiliation(s)
- Marisol Delea
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Lucia S. Massara
- Hospital de Alta Complejidad en Red El Cruce—SAMIC. Av. Calchaquí 5401, Florencio Varela 1888, Argentina; (L.S.M.); (J.O.); (P.B.)
| | - Lucia D. Espeche
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - María Paz Bidondo
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
- Unidad Académica de Histologia, Embriologia, Biologia Celular y Genética, Facultad de Medicina UBA, Paraguay 2155, Buenos Aires 1121, Argentina
| | - Pablo Barbero
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Jaen Oliveri
- Hospital de Alta Complejidad en Red El Cruce—SAMIC. Av. Calchaquí 5401, Florencio Varela 1888, Argentina; (L.S.M.); (J.O.); (P.B.)
| | - Paloma Brun
- Hospital de Alta Complejidad en Red El Cruce—SAMIC. Av. Calchaquí 5401, Florencio Varela 1888, Argentina; (L.S.M.); (J.O.); (P.B.)
| | - Mónica Fabro
- Novagen, Viamonte 1430, Buenos Aires 1055, Argentina; (M.F.); (M.G.); (C.S.F.)
| | - Micaela Galain
- Novagen, Viamonte 1430, Buenos Aires 1055, Argentina; (M.F.); (M.G.); (C.S.F.)
| | | | - Melisa Taboas
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Carlos D. Bruque
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Jorge E. Kolomenski
- Departamento de Fisiología, Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Facultad de Ciencias Exactas y Naturales-UBA, Intendente Güiraldes 2160, Buenos Aires 1428, Argentina;
| | - Agustín Izquierdo
- Centro de Investigaciones Endocrinológicas “Dr. César Bergadá”. Gallo 1330, Buenos Aires 1425, Argentina;
| | - Ariel Berenstein
- Instituto Multidisciplinario de Investigaciones en Patologías Pediátricas, Gallo 1330, Buenos Aires 1425, Argentina;
| | - Viviana Cosentino
- Hospital Interzonal General de Agudos Luisa Cravenna de Gandulfo, Balcarce 351, Lomas de Zamora 1832, Argentina;
| | - Celeste Martinoli
- Hospital Sor Maria Ludovica, Calle 14 1631, La Plata 1904, Argentina;
| | - Mariana Vilas
- Hospital Materno Infantil Ramón Sardá, Esteban de Luca 2151, Buenos Aires 1246, Argentina; (M.V.); (M.R.); (L.F.)
| | - Mónica Rittler
- Hospital Materno Infantil Ramón Sardá, Esteban de Luca 2151, Buenos Aires 1246, Argentina; (M.V.); (M.R.); (L.F.)
| | - Rodrigo Mendez
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Lilian Furforo
- Hospital Materno Infantil Ramón Sardá, Esteban de Luca 2151, Buenos Aires 1246, Argentina; (M.V.); (M.R.); (L.F.)
| | - Rosa Liascovich
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Boris Groisman
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Sandra Rozental
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
| | - Liliana Dain
- Centro Nacional de Genética Médica “Dr. Eduardo Castilla”- ANLIS “Dr. Carlos G. Malbrán”, Avda. Las Heras 2670, Buenos Aires 1425, Argentina; (M.D.); (L.D.E.); (M.P.B.); (P.B.); (M.T.); (C.D.B.); (R.M.); (R.L.); (B.G.); (S.R.)
- Departamento de Fisiología, Biología Molecular y Celular, Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Facultad de Ciencias Exactas y Naturales-UBA, Intendente Güiraldes 2160, Buenos Aires 1428, Argentina;
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Fanelli A, Vannelli S, Babu D, Mellone S, Cucci A, Monzani A, Al Essa W, Secco A, Follenzi A, Bellone S, Prodam F, Giordano M. Copy number variations residing outside the SHOX enhancer region are involved in Short Stature and Léri-Weill dyschondrosteosis. Mol Genet Genomic Med 2021; 10:e1793. [PMID: 34811950 PMCID: PMC8801136 DOI: 10.1002/mgg3.1793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 07/19/2021] [Accepted: 08/16/2021] [Indexed: 11/25/2022] Open
Abstract
Background SHOX enhancer CNVs, affecting one or more of the seven recognized evolutionary conserved non‐coding elements (CNEs) represent one of the most frequent cause of SHOX‐haploinsufficiency. During the diagnostic workflow deletions/duplications have been identified downstream SHOX not including any of the these CNEs. Methods Fine tiling aCGH and breakpoint PCR were used to characterize the critical interval and to search for novel alterations in a cohort of selected patients. Results Screening of 252 controls provided evidence that duplications in this area represent likely benign variants whereas none of the deletions were detected. These findings suggested that other alterations relevant for SHOX‐haploinsufficiency might be missed by the standard diagnostic methods. To identify such undisclosed elements, the aCGH was used to reanalyze 52 unresolved cases with clinical features strongly suggestive of SHOX‐haploinsufficiency. This analysis followed by the screening of 210 patients detected two partially overlapping small deletions of ~12 and ~8 kb in four unrelated individuals, approximately 15 kb downstream SHOX, that were absent in 720 normal stature individuals. Conclusion Our results strengthen the hypothesis that alterations of yet unidentified cis‐regulatory elements residing outside those investigated through conventional methods, might explain the phenotype in ISS/LWD patients thus enlarging the spectrum of variants contributing to SHOX‐haploinsufficiency.
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Affiliation(s)
- Antonella Fanelli
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy
| | - Silvia Vannelli
- Endocrinologia Pediatrica, Dipartimento di Pediatria e Specialità Pediatriche, Ospedale Regina Margherita, Citta della Salute e della Scienza, Torino, Italy
| | - Deepak Babu
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy
| | - Simona Mellone
- Laboratorio di Genetica, S.C.D.U Biochimica Clinica, Azienda Ospedaliera Universitaria "Maggiore della Carità", Novara, Italy
| | - Alessia Cucci
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy
| | - Alice Monzani
- Divisione di Pediatria, AOU "Maggiore della Carità", Novara, Italy
| | - Wael Al Essa
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy
| | - Andrea Secco
- SC Pediatria e DEA Pediatrico, Azienda Ospedaliera SS. Antonio e Biagio e Cesare Arrigo, Alessandria, Italy
| | - Antonia Follenzi
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy
| | - Simonetta Bellone
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy.,Divisione di Pediatria, AOU "Maggiore della Carità", Novara, Italy
| | - Flavia Prodam
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy.,Divisione di Endocrinologia, AOU "Maggiore della Carità", Novara, Italy
| | - Mara Giordano
- Dipartimento di Scienze della Salute, Università del Piemonte Orientale, Novara, Italy.,Laboratorio di Genetica, S.C.D.U Biochimica Clinica, Azienda Ospedaliera Universitaria "Maggiore della Carità", Novara, Italy
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Chen CP, Chan CH, Chern SR, Wu PS, Chen SW, Wu FT, Town DD, Lee MS, Wang W. Prenatal diagnosis and molecular cytogenetic characterization of a small supernumerary marker chromosome derived from chromosome 15 in a pregnancy associated with recurrent Down syndrome. Taiwan J Obstet Gynecol 2021; 60:152-156. [PMID: 33494992 DOI: 10.1016/j.tjog.2020.11.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2020] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVE We present prenatal diagnosis and molecular cytogenetic characterization of a small supernumerary marker chromosome (sSMC) derived from chromosome 15 in a pregnancy associated with recurrent Down syndrome. CASE REPORT A 33-year-old, gravida 4, para 2, woman underwent amniocentesis at 16 weeks of gestation because of a previous child with Down syndrome and a karyotype of 46,XY,der(14;21)(q10; q10),+21. In this pregnancy, amniocentesis revealed a karyotype of 47,XX,+21[12]/48,XX,+21,+mar[3]. The parental karyotypes were normal. The pregnancy was terminated, and a malformed fetus was delivered with characteristic craniofacial appearance of Down syndrome and hypoplastic middle phalanx of the fifth fingers. The placenta had a karyotype of 47,XX,+21[37]/48,XX,+21,+mar[3]. The umbilical cord had a karyotype of 47,XX,+21[38]/48,XX,+21,+mar[2]. In addition to trisomy 21, array comparative genomic hybridization (aCGH) on the DNA extracted from umbilical cord revealed 40∼50% mosaicism for a 2.604-Mb duplication of 15q25.2-q25.3, or arr 15q25.2q25.3 (83,229,665-85,834,131) × 2.4 [GRCh37 (hg19)] encompassing 19 Online Mendelian Inheritance in Man (OMIM) genes. Quantitative fluorescent polymerase chain reaction (QF-PCR) using the DNAs extracted from cultured amniocytes and parental bloods revealed maternal origin of the sSMC(15) and the extra chromosome 21. CONCLUSION aCGH is useful for identification of the nature of sSMC, and QF-PCR is useful for determination of the parental origin of the aberrant chromosomes.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan; Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung, Taiwan.
| | - Chia-Hao Chan
- Department of Obstetrics and Gynecology, Hsinchu MacKay Memorial Hospital, Hsinchu, Taiwan
| | - Schu-Rern Chern
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | | | - Shin-Wen Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Fang-Tzu Wu
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Dai-Dyi Town
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Meng-Shan Lee
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
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Hoffmann S, Roeth R, Diebold S, Gogel J, Hassel D, Just S, Rappold GA. Identification and Tissue-Specific Characterization of Novel SHOX-Regulated Genes in Zebrafish Highlights SOX Family Members Among Other Genes. Front Genet 2021; 12:688808. [PMID: 34122528 PMCID: PMC8191631 DOI: 10.3389/fgene.2021.688808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/27/2021] [Indexed: 02/01/2023] Open
Abstract
SHOX deficiency causes a spectrum of clinical phenotypes related to skeletal dysplasia and short stature, including Léri-Weill dyschondrosteosis, Langer mesomelic dysplasia, Turner syndrome, and idiopathic short stature. SHOX controls chondrocyte proliferation and differentiation, bone maturation, and cellular growth arrest and apoptosis via transcriptional regulation of its direct target genes NPPB, FGFR3, and CTGF. However, our understanding of SHOX-related pathways is still incomplete. To elucidate the underlying molecular mechanisms and to better understand the broad phenotypic spectrum of SHOX deficiency, we aimed to identify novel SHOX targets. We analyzed differentially expressed genes in SHOX-overexpressing human fibroblasts (NHDF), and confirmed the known SHOX target genes NPPB and FGFR among the most strongly regulated genes, together with 143 novel candidates. Altogether, 23 genes were selected for further validation, first by whole-body characterization in developing shox-deficient zebrafish embryos, followed by tissue-specific expression analysis in three shox-expressing zebrafish tissues: head (including brain, pharyngeal arches, eye, and olfactory epithelium), heart, and pectoral fins. Most genes were physiologically relevant in the pectoral fins, while only few genes were also significantly regulated in head and heart tissue. Interestingly, multiple sox family members (sox5, sox6, sox8, and sox18) were significantly dysregulated in shox-deficient pectoral fins together with other genes (nppa, nppc, cdkn1a, cdkn1ca, cyp26b1, and cy26c1), highlighting an important role for these genes in shox-related growth disorders. Network-based analysis integrating data from the Ingenuity pathways revealed that most of these genes act in a common network. Our results provide novel insights into the genetic pathways and molecular events leading to the clinical manifestation of SHOX deficiency.
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Affiliation(s)
- Sandra Hoffmann
- Department of Human Molecular Genetics, Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Ralph Roeth
- Department of Human Molecular Genetics, Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany.,nCounter Core Facility, Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Sabrina Diebold
- Clinic for Internal Medicine II - Molecular Cardiology, University Hospital Ulm, Ulm, Germany
| | - Jasmin Gogel
- Department of Human Molecular Genetics, Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - David Hassel
- Department of Internal Medicine III - Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Steffen Just
- Clinic for Internal Medicine II - Molecular Cardiology, University Hospital Ulm, Ulm, Germany
| | - Gudrun A Rappold
- Department of Human Molecular Genetics, Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Heidelberg, Germany
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Variants in the 5'UTR reduce SHOX expression and contribute to SHOX haploinsufficiency. Eur J Hum Genet 2020; 29:110-121. [PMID: 32647378 PMCID: PMC7852508 DOI: 10.1038/s41431-020-0676-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 06/08/2020] [Accepted: 06/23/2020] [Indexed: 11/08/2022] Open
Abstract
SHOX haploinsufficiency causes 70-90% of Léri-Weill dyschondrosteosis (LWD) and 2-10% of idiopathic short stature (ISS). Deletions removing the entire gene or enhancers and point mutations in the coding region represent a well-established cause of haploinsufficiency. During diagnostic genetic testing on ISS/LWD patients, in addition to classic SHOX defects, five 5'UTR variants (c.-58G > T, c.-55C > T, c.-51G > A, c.-19G > A, and c.-9del), were detected whose pathogenetic role was unclear and were thus classified as VUS (Variants of Uncertain Significance). The purpose of the present study was to investigate the role of these noncoding variations in SHOX haploinsufficiency. The variants were tested for their ability to interfere with correct gene expression of a regulated reporter gene (luciferase assay). The negative effect on the mRNA splicing predicted in silico for c.-19G > A was assayed in vitro through a minigene splicing assay. The luciferase assay showed that c.-51G > A, c.-19G > A, and c.-9del significantly reduce luciferase activity by 60, 35, and 40% at the homozygous state. Quantification of the luciferase mRNA showed that c.-51G > A and c.-9del might interfere with the correct SHOX expression mainly at the post-transcriptional level. The exon trapping assay demonstrated that c.-19G > A determines the creation of a new branch site causing an aberrant mRNA splicing. In conclusion, this study allowed us to reclassify two of the 5'UTR variants identified during SHOX diagnostic screening as likely pathogenic, one remains as a VUS, and two as likely benign variants. This analysis for the first time expands the spectrum of the genetic causes of SHOX haploinsufficiency to noncoding variations in the 5'UTR.
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Sadler B, Haller G, Antunes L, Nikolov M, Amarillo I, Coe B, Dobbs MB, Gurnett CA. Rare and de novo duplications containing SHOX in clubfoot. J Med Genet 2020; 57:851-857. [PMID: 32518174 PMCID: PMC7688552 DOI: 10.1136/jmedgenet-2020-106842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 11/12/2022]
Abstract
Introduction Congenital clubfoot is a common birth defect that affects at least 0.1% of all births. Nearly 25% cases are familial and the remaining are sporadic in inheritance. Copy number variants (CNVs) involving transcriptional regulators of limb development, including PITX1 and TBX4, have previously been shown to cause familial clubfoot, but much of the heritability remains unexplained. Methods Exome sequence data from 816 unrelated clubfoot cases and 2645 in-house controls were analysed using coverage data to identify rare CNVs. The precise size and location of duplications were then determined using high-density Affymetrix Cytoscan chromosomal microarray (CMA). Segregation in families and de novo status were determined using qantitative PCR. Results Chromosome Xp22.33 duplications involving SHOX were identified in 1.1% of cases (9/816) compared with 0.07% of in-house controls (2/2645) (p=7.98×10−5, OR=14.57) and 0.27% (38/13592) of Atherosclerosis Risk in Communities/the Wellcome Trust Case Control Consortium 2 controls (p=0.001, OR=3.97). CMA validation confirmed an overlapping 180.28 kb duplicated region that included SHOX exons as well as downstream non-coding regions. In four of six sporadic cases where DNA was available for unaffected parents, the duplication was de novo. The probability of four de novo mutations in SHOX by chance in a cohort of 450 sporadic clubfoot cases is 5.4×10–10. Conclusions Microduplications of the pseudoautosomal chromosome Xp22.33 region (PAR1) containing SHOX and downstream enhancer elements occur in ~1% of patients with clubfoot. SHOX and regulatory regions have previously been implicated in skeletal dysplasia as well as idiopathic short stature, but have not yet been reported in clubfoot. SHOX duplications likely contribute to clubfoot pathogenesis by altering early limb development.
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Affiliation(s)
- Brooke Sadler
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
| | - Gabe Haller
- Department of Orthopedic Surgery, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
| | - Lilian Antunes
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
| | - Momchil Nikolov
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
| | - Ina Amarillo
- Department of Pathology and Immunology, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
| | - Bradley Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew B Dobbs
- Department of Orthopedic Surgery, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
| | - Christina A Gurnett
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
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Vendramini-Pittoli S, Candido-Souza RM, Quiezi RG, Zechi-Ceide RM, Kokitsu-Nakata NM, Jehee FS, Ribeiro-Bicudo LA, FitzPatrick DR, Guion-Almeida ML, Richieri-Costa A. Microphthalmia, Linear Skin Defects, Callosal Agenesis, and Cleft Palate in a Patient with Deletion at Xp22.3p22.2. J Pediatr Genet 2020; 9:258-262. [PMID: 32765930 DOI: 10.1055/s-0039-3402047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/07/2019] [Indexed: 01/23/2023]
Abstract
The authors describe the clinical findings observed in a Brazilian girl that are suggestive of microphthalmia and linear skin defects (MLS) also known as MIDAS syndrome (OMIM #309801). She also presented with short stature, agenesis of corpus callosum, cleft palate, enamel defects, and genitourinary anomalies, which are rarely reported within the clinical spectrum of MLS. The 11,5 Mb deletion in Xp22.3p22.2 observed in the patient includes the entire HCCS gene (responsible for the MLS phenotype) and also encompasses several other genes involved with behavioral phenotypes, craniofacial and central nervous system development such as MID1, NLGN4X, AMELX , ARHGAP6, and TBL1X. The whole clinical features of our proband possibly represents an unusual MLS syndromic phenotype caused by an Xp22.3p22.2 continuous gene deletion.
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Affiliation(s)
- Siulan Vendramini-Pittoli
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | - Rosana Maria Candido-Souza
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | - Rodrigo Gonçalves Quiezi
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Roseli Maria Zechi-Ceide
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | - Nancy Mizue Kokitsu-Nakata
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | | | | | - David R FitzPatrick
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom
| | - Maria Leine Guion-Almeida
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | - Antonio Richieri-Costa
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
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