1
|
Onore ME, Caiazza M, Farina A, Scarano G, Budillon A, Borrelli RN, Limongelli G, Nigro V, Piluso G. A Novel Homozygous Loss-of-Function Variant in SPRED2 Causes Autosomal Recessive Noonan-like Syndrome. Genes (Basel) 2023; 15:32. [PMID: 38254922 PMCID: PMC10815364 DOI: 10.3390/genes15010032] [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: 12/04/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Noonan syndrome is an autosomal dominant developmental disorder characterized by peculiar facial dysmorphisms, short stature, congenital heart defects, and hypertrophic cardiomyopathy. In 2001, PTPN11 was identified as the first Noonan syndrome gene and is responsible for the majority of Noonan syndrome cases. Over the years, several other genes involved in Noonan syndrome (KRAS, SOS1, RAF1, MAP2K1, BRAF, NRAS, RIT1, and LZTR1) have been identified, acting at different levels of the RAS-mitogen-activated protein kinase pathway. Recently, SPRED2 was recognized as a novel Noonan syndrome gene with autosomal recessive inheritance, and only four families have been described to date. Here, we report the first Italian case, a one-year-old child with left ventricular hypertrophy, moderate pulmonary valve stenosis, and atrial septal defect, with a clinical suspicion of RASopathy supported by the presence of typical Noonan-like facial features and short stature. Exome sequencing identified a novel homozygous loss-of-function variant in the exon 3 of SPRED2 (NM_181784.3:c.325del; p.Arg109Glufs*7), likely causing nonsense-mediated decay. Our results and the presented clinical data may help us to further understand and dissect the genetic heterogeneity of Noonan syndrome.
Collapse
Affiliation(s)
- Maria Elena Onore
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.E.O.); (A.F.); (A.B.); (R.N.B.); (V.N.)
| | - Martina Caiazza
- Inherited and Rare Cardiovascular Diseases Unit, Department of Translational Medical Sciences, University of Campania “Luigi Vanvitelli”, Monaldi Hospital, 80131 Naples, Italy; (M.C.); (G.S.); (G.L.)
| | - Antonella Farina
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.E.O.); (A.F.); (A.B.); (R.N.B.); (V.N.)
| | - Gioacchino Scarano
- Inherited and Rare Cardiovascular Diseases Unit, Department of Translational Medical Sciences, University of Campania “Luigi Vanvitelli”, Monaldi Hospital, 80131 Naples, Italy; (M.C.); (G.S.); (G.L.)
- Medical Genetics Unit, AORN “San Pio”, Hospital “G. Rummo”, 82100 Benevento, Italy
| | - Alberto Budillon
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.E.O.); (A.F.); (A.B.); (R.N.B.); (V.N.)
| | - Rossella Nicoletta Borrelli
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.E.O.); (A.F.); (A.B.); (R.N.B.); (V.N.)
| | - Giuseppe Limongelli
- Inherited and Rare Cardiovascular Diseases Unit, Department of Translational Medical Sciences, University of Campania “Luigi Vanvitelli”, Monaldi Hospital, 80131 Naples, Italy; (M.C.); (G.S.); (G.L.)
- Institute of Cardiovascular Science, University College London and St. Bartholomew’s Hospital, London E1 4NS, UK
| | - Vincenzo Nigro
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.E.O.); (A.F.); (A.B.); (R.N.B.); (V.N.)
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Giulio Piluso
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.E.O.); (A.F.); (A.B.); (R.N.B.); (V.N.)
| |
Collapse
|
2
|
Correia-Costa GR, dos Santos AM, de Leeuw N, Rigatto SZP, Belangero VMS, Steiner CE, Gil-da-Silva-Lopes VL, Vieira TP. Dual Molecular Diagnoses of Recessive Disorders in a Child from Consanguineous Parents: Case Report and Literature Review. Genes (Basel) 2022; 13:2377. [PMID: 36553645 PMCID: PMC9778442 DOI: 10.3390/genes13122377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
The widespread use of whole exome sequencing (WES) resulted in the discovery of multilocus pathogenic variations (MPV), defined as two or more distinct or overlapping Mendelian disorders occurring in a patient, leading to a blended phenotype. In this study, we report on a child with autosomal recessive primary microcephaly-5 (MCPH5) and nephropathic cystinosis. The proband is the first child of consanguineous parents, presenting a complex phenotype including neurodevelopmental delay, microcephaly, growth restriction, significant delay of bone maturation, lissencephaly, and abnormality of neuronal migration, photophobia, and renal tubular acidosis. WES revealed two pathogenic and homozygous variants: a c.4174C>T variant in the ASPM gene and a c.382C>T variant in the CTNS gene, explaining the complex phenotype. The literature review showed that most of the patients harboring two variants in recessive disease genes are born to consanguineous parents. To the best of our knowledge, the patient herein described is the first one harboring pathogenic variants in both the ASPM and CTNS genes. These findings highlight the importance of searching for MPV in patients with complex phenotypes investigated by genome-wide testing methods, especially for those patients born to consanguineous parents.
Collapse
Affiliation(s)
- Gabriela Roldão Correia-Costa
- Department of Translational Medicine—Medical Genetics and Genomic Medicine, School of Medical Sciences, State University of Campinas, Campinas 13083-887, São Paulo, Brazil
| | - Ana Mondadori dos Santos
- Department of Translational Medicine—Medical Genetics and Genomic Medicine, School of Medical Sciences, State University of Campinas, Campinas 13083-887, São Paulo, Brazil
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Sumara Zuanazi Pinto Rigatto
- Department of Pediatrics, School of Medical Sciences, State University of Campinas, Campinas 13083-887, São Paulo, Brazil
| | - Vera Maria Santoro Belangero
- Department of Pediatrics, School of Medical Sciences, State University of Campinas, Campinas 13083-887, São Paulo, Brazil
| | - Carlos Eduardo Steiner
- Department of Translational Medicine—Medical Genetics and Genomic Medicine, School of Medical Sciences, State University of Campinas, Campinas 13083-887, São Paulo, Brazil
| | - Vera Lúcia Gil-da-Silva-Lopes
- Department of Translational Medicine—Medical Genetics and Genomic Medicine, School of Medical Sciences, State University of Campinas, Campinas 13083-887, São Paulo, Brazil
| | - Társis Paiva Vieira
- Department of Translational Medicine—Medical Genetics and Genomic Medicine, School of Medical Sciences, State University of Campinas, Campinas 13083-887, São Paulo, Brazil
| |
Collapse
|
3
|
Correia-Costa GR, de Leeuw N, Pfundt R, Sgardioli IC, Dos Santos AP, de Lima Santos M, Gil-da-Silva-Lopes VL, Vieira TP. Biallelic frameshift variant in the TBC1D2B gene in two siblings with progressive gingival overgrowth, fibrous dysplasia of face, and mental deterioration. Clin Genet 2022; 102:537-542. [PMID: 36029130 DOI: 10.1111/cge.14215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 01/27/2023]
Abstract
Biallelic loss-of-function variants in the TBC1D2B gene were recently reported as a cause of a neurodevelopmental disorder with seizures and gingival overgrowth. Here, we report two male siblings with the similar clinical characteristics. They started with gingival overgrowth and bilateral growth of soft tissues in the malar region at 3 years of age, which evolved with significant maxillary hypertrophy and compression of the brainstem due to fibrous dysplasia of facial bones. After disease evolution, they presented with mental deterioration, limb tremors, and gait ataxia. One of them also presented with seizures. Whole exome sequencing revealed a novel biallelic frameshift variant [c.595del; p.(Val199Trpfs*22)] in the TBC1D2B gene in both patients, which was confirmed and found in heterozygous state in each of their parents. There are strong similarities in clinical characteristics, age of onset, and evolution between the patients described here and cases reported in the literature, including cherubism-like phenotype with progressive gingival overgrowth and seizures. This is the fourth family in the world in which a biallelic loss-of-function variant in the TBC1D2B gene is associated with this phenotype. These results support that loss of TBC1D2B is the cause of this rare condition.
Collapse
Affiliation(s)
- Gabriela Roldão Correia-Costa
- Department of Translational Medicine - Laboratory of Human Cytogenetics and Cytogenomics, School of Medical Sciences, State University of Campinas, São Paulo, Brazil
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ilária Cristina Sgardioli
- Department of Translational Medicine - Laboratory of Human Cytogenetics and Cytogenomics, School of Medical Sciences, State University of Campinas, São Paulo, Brazil
| | - Ana Paula Dos Santos
- Department of Translational Medicine - Laboratory of Human Cytogenetics and Cytogenomics, School of Medical Sciences, State University of Campinas, São Paulo, Brazil
| | - Marilza de Lima Santos
- Department of Translational Medicine - Laboratory of Human Cytogenetics and Cytogenomics, School of Medical Sciences, State University of Campinas, São Paulo, Brazil
| | - Vera Lúcia Gil-da-Silva-Lopes
- Department of Translational Medicine - Laboratory of Human Cytogenetics and Cytogenomics, School of Medical Sciences, State University of Campinas, São Paulo, Brazil
| | - Társis Paiva Vieira
- Department of Translational Medicine - Laboratory of Human Cytogenetics and Cytogenomics, School of Medical Sciences, State University of Campinas, São Paulo, Brazil
| |
Collapse
|
4
|
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.
Collapse
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;
| | | |
Collapse
|