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Gupta V, Ben-Mahmoud A, Ku B, Velayutham D, Jan Z, Yousef Aden A, Kubbar A, Alshaban F, Stanton LW, Jithesh PV, Layman LC, Kim HG. Identification of two novel autism genes, TRPC4 and SCFD2, in Qatar simplex families through exome sequencing. Front Psychiatry 2023; 14:1251884. [PMID: 38025430 PMCID: PMC10644705 DOI: 10.3389/fpsyt.2023.1251884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
This study investigated the genetic underpinnings of autism spectrum disorder (ASD) in a Middle Eastern cohort in Qatar using exome sequencing. The study identified six candidate autism genes in independent simplex families, including both four known and two novel autosomal dominant and autosomal recessive genes associated with ASD. The variants consisted primarily of de novo and homozygous missense and splice variants. Multiple individuals displayed more than one candidate variant, suggesting the potential involvement of digenic or oligogenic models. These variants were absent in the Genome Aggregation Database (gnomAD) and exhibited extremely low frequencies in the local control population dataset. Two novel autism genes, TRPC4 and SCFD2, were discovered in two Qatari autism individuals. Furthermore, the D651A substitution in CLCN3 and the splice acceptor variant in DHX30 were identified as likely deleterious mutations. Protein modeling was utilized to evaluate the potential impact of three missense variants in DEAF1, CLCN3, and SCFD2 on their respective structures and functions, which strongly supported the pathogenic natures of these variants. The presence of multiple de novo mutations across trios underscored the significant contribution of de novo mutations to the genetic etiology of ASD. Functional assays and further investigations are necessary to confirm the pathogenicity of the identified genes and determine their significance in ASD. Overall, this study sheds light on the genetic factors underlying ASD in Qatar and highlights the importance of considering diverse populations in ASD research.
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Affiliation(s)
- Vijay Gupta
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Afif Ben-Mahmoud
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Dinesh Velayutham
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Zainab Jan
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Abdi Yousef Aden
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Ahmad Kubbar
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Fouad Alshaban
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Lawrence W. Stanton
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Puthen Veettil Jithesh
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Lawrence C. Layman
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Augusta University, Augusta, GA, United States
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, GA, United States
| | - Hyung-Goo Kim
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
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4
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Pascual P, Tenorio-Castano J, Mignot C, Afenjar A, Arias P, Gallego-Zazo N, Parra A, Miranda L, Cazalla M, Silván C, Heron D, Keren B, Popa I, Palomares M, Rikeros E, Ramos FJ, Almoguera B, Ayuso C, Swafiri ST, Barbero AIS, Srinivasan VM, Gowda VK, Morleo M, Nigro V, D’Arrigo S, Ciaccio C, Martin Mesa C, Paumard B, Guillen G, Anton ATS, Jimenez MD, Seidel V, Suárez J, Cormier-Daire V, Consortium TSOGRI, Nevado J, Lapunzina P. Snijders Blok-Campeau Syndrome: Description of 20 Additional Individuals with Variants in CHD3 and Literature Review. Genes (Basel) 2023; 14:1664. [PMID: 37761804 PMCID: PMC10530855 DOI: 10.3390/genes14091664] [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: 06/22/2023] [Revised: 08/01/2023] [Accepted: 08/08/2023] [Indexed: 09/29/2023] Open
Abstract
Snijders Blok-Campeau syndrome (SNIBCPS, OMIM# 618205) is an extremely infrequent disease with only approximately 60 cases reported so far. SNIBCPS belongs to the group of neurodevelopmental disorders (NDDs). Clinical features of patients with SNIBCPS include global developmental delay, intellectual disability, speech and language difficulties and behavioral disorders like autism spectrum disorder. In addition, patients with SNIBCPS exhibit typical dysmorphic features including macrocephaly, hypertelorism, sparse eyebrows, broad forehead, prominent nose and pointed chin. The severity of the neurological effects as well as the presence of other features is variable among subjects. SNIBCPS is caused likely by pathogenic and pathogenic variants in CHD3 (Chromodomain Helicase DNA Binding Protein 3), which seems to be involved in chromatin remodeling by deacetylating histones. Here, we report 20 additional patients with clinical features compatible with SNIBCPS from 17 unrelated families with confirmed likely pathogenic/pathogenic variants in CHD3. Patients were analyzed by whole exome sequencing and segregation studies were performed by Sanger sequencing. Patients in this study showed different pathogenic variants affecting several functional domains of the protein. Additionally, none of the variants described here were reported in control population databases, and most computational predictors suggest that they are deleterious. The most common clinical features of the whole cohort of patients are global developmental delay (98%) and speech disorder/delay (92%). Other frequent features (51-74%) include intellectual disability, hypotonia, hypertelorism, abnormality of vision, macrocephaly and prominent forehead, among others. This study expands the number of individuals with confirmed SNIBCPS due to pathogenic or likely pathogenic variants in CHD3. Furthermore, we add evidence of the importance of the application of massive parallel sequencing for NDD patients for whom the clinical diagnosis might be challenging and where deep phenotyping is extremely useful to accurately manage and follow up the patients.
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Affiliation(s)
- Patricia Pascual
- CIBERER, Center for Biomedical Research in Rare Diseases Network, 28029 Madrid, Spain; (P.P.); (J.T.-C.); (P.A.); (N.G.-Z.); (A.P.); (L.M.); (M.P.); (E.R.); (F.J.R.); (B.A.); (C.A.); (S.T.S.); (A.I.S.B.); (The SOGRI Consortium); (J.N.)
- INGEMM-IdiPaz, Institute of Medical and Molecular Genetics, 28046 Madrid, Spain; (M.C.); (C.S.)
- ITHACA, European Reference Network, 1140 Brussels, Belgium; (S.D.); (C.C.)
| | - Jair Tenorio-Castano
- CIBERER, Center for Biomedical Research in Rare Diseases Network, 28029 Madrid, Spain; (P.P.); (J.T.-C.); (P.A.); (N.G.-Z.); (A.P.); (L.M.); (M.P.); (E.R.); (F.J.R.); (B.A.); (C.A.); (S.T.S.); (A.I.S.B.); (The SOGRI Consortium); (J.N.)
- INGEMM-IdiPaz, Institute of Medical and Molecular Genetics, 28046 Madrid, Spain; (M.C.); (C.S.)
- ITHACA, European Reference Network, 1140 Brussels, Belgium; (S.D.); (C.C.)
| | - Cyril Mignot
- Département de Génétique, APHP Sorbonne Université, 75013 Paris, France; (D.H.); (C.M.); (A.A.); (B.K.); (I.P.)
- Centre de Réference Déficiences Intellectuelles de Causes Rares, 75013 Paris, France
| | - Alexandra Afenjar
- Département de Génétique, APHP Sorbonne Université, 75013 Paris, France; (D.H.); (C.M.); (A.A.); (B.K.); (I.P.)
- Centre de Réference Déficiences Intellectuelles de Causes Rares, 75013 Paris, France
| | - Pedro Arias
- CIBERER, Center for Biomedical Research in Rare Diseases Network, 28029 Madrid, Spain; (P.P.); (J.T.-C.); (P.A.); (N.G.-Z.); (A.P.); (L.M.); (M.P.); (E.R.); (F.J.R.); (B.A.); (C.A.); (S.T.S.); (A.I.S.B.); (The SOGRI Consortium); (J.N.)
- INGEMM-IdiPaz, Institute of Medical and Molecular Genetics, 28046 Madrid, Spain; (M.C.); (C.S.)
- ITHACA, European Reference Network, 1140 Brussels, Belgium; (S.D.); (C.C.)
| | - Natalia Gallego-Zazo
- CIBERER, Center for Biomedical Research in Rare Diseases Network, 28029 Madrid, Spain; (P.P.); (J.T.-C.); (P.A.); (N.G.-Z.); (A.P.); (L.M.); (M.P.); (E.R.); (F.J.R.); (B.A.); (C.A.); (S.T.S.); (A.I.S.B.); (The SOGRI Consortium); (J.N.)
- INGEMM-IdiPaz, Institute of Medical and Molecular Genetics, 28046 Madrid, Spain; (M.C.); (C.S.)
- ITHACA, European Reference Network, 1140 Brussels, Belgium; (S.D.); (C.C.)
| | - Alejandro Parra
- CIBERER, Center for Biomedical Research in Rare Diseases Network, 28029 Madrid, Spain; (P.P.); (J.T.-C.); (P.A.); (N.G.-Z.); (A.P.); (L.M.); (M.P.); (E.R.); (F.J.R.); (B.A.); (C.A.); (S.T.S.); (A.I.S.B.); (The SOGRI Consortium); (J.N.)
- INGEMM-IdiPaz, Institute of Medical and Molecular Genetics, 28046 Madrid, Spain; (M.C.); (C.S.)
- ITHACA, European Reference Network, 1140 Brussels, Belgium; (S.D.); (C.C.)
| | - Lucia Miranda
- CIBERER, Center for Biomedical Research in Rare Diseases Network, 28029 Madrid, Spain; (P.P.); (J.T.-C.); (P.A.); (N.G.-Z.); (A.P.); (L.M.); (M.P.); (E.R.); (F.J.R.); (B.A.); (C.A.); (S.T.S.); (A.I.S.B.); (The SOGRI Consortium); (J.N.)
- INGEMM-IdiPaz, Institute of Medical and Molecular Genetics, 28046 Madrid, Spain; (M.C.); (C.S.)
- ITHACA, European Reference Network, 1140 Brussels, Belgium; (S.D.); (C.C.)
| | - Mario Cazalla
- INGEMM-IdiPaz, Institute of Medical and Molecular Genetics, 28046 Madrid, Spain; (M.C.); (C.S.)
| | - Cristina Silván
- INGEMM-IdiPaz, Institute of Medical and Molecular Genetics, 28046 Madrid, Spain; (M.C.); (C.S.)
| | - Delphine Heron
- Département de Génétique, APHP Sorbonne Université, 75013 Paris, France; (D.H.); (C.M.); (A.A.); (B.K.); (I.P.)
- Centre de Réference Déficiences Intellectuelles de Causes Rares, 75013 Paris, France
| | - Boris Keren
- Département de Génétique, APHP Sorbonne Université, 75013 Paris, France; (D.H.); (C.M.); (A.A.); (B.K.); (I.P.)
| | - Ioana Popa
- Département de Génétique, APHP Sorbonne Université, 75013 Paris, France; (D.H.); (C.M.); (A.A.); (B.K.); (I.P.)
| | - María Palomares
- CIBERER, Center for Biomedical Research in Rare Diseases Network, 28029 Madrid, Spain; (P.P.); (J.T.-C.); (P.A.); (N.G.-Z.); (A.P.); (L.M.); (M.P.); (E.R.); (F.J.R.); (B.A.); (C.A.); (S.T.S.); (A.I.S.B.); (The SOGRI Consortium); (J.N.)
- INGEMM-IdiPaz, Institute of Medical and Molecular Genetics, 28046 Madrid, Spain; (M.C.); (C.S.)
- ITHACA, European Reference Network, 1140 Brussels, Belgium; (S.D.); (C.C.)
| | - Emi Rikeros
- CIBERER, Center for Biomedical Research in Rare Diseases Network, 28029 Madrid, Spain; (P.P.); (J.T.-C.); (P.A.); (N.G.-Z.); (A.P.); (L.M.); (M.P.); (E.R.); (F.J.R.); (B.A.); (C.A.); (S.T.S.); (A.I.S.B.); (The SOGRI Consortium); (J.N.)
- INGEMM-IdiPaz, Institute of Medical and Molecular Genetics, 28046 Madrid, Spain; (M.C.); (C.S.)
- ITHACA, European Reference Network, 1140 Brussels, Belgium; (S.D.); (C.C.)
| | - Feliciano J. Ramos
- CIBERER, Center for Biomedical Research in Rare Diseases Network, 28029 Madrid, Spain; (P.P.); (J.T.-C.); (P.A.); (N.G.-Z.); (A.P.); (L.M.); (M.P.); (E.R.); (F.J.R.); (B.A.); (C.A.); (S.T.S.); (A.I.S.B.); (The SOGRI Consortium); (J.N.)
- Unidad de Genética Clínica, Servicio de Pediatría, Hospital Clínico Universitario ‘Lozano Blesa’, Facultad de Medicina, Universidad de Zaragoza, IIS-Aragón Grupo B32-20R, 50013 Zaragoza, Spain
| | - Berta Almoguera
- CIBERER, Center for Biomedical Research in Rare Diseases Network, 28029 Madrid, Spain; (P.P.); (J.T.-C.); (P.A.); (N.G.-Z.); (A.P.); (L.M.); (M.P.); (E.R.); (F.J.R.); (B.A.); (C.A.); (S.T.S.); (A.I.S.B.); (The SOGRI Consortium); (J.N.)
- Department of Genetics and Genomics, Fundación Jiménez Díaz University Hospital, Health Research Institute Fundación Jiménez Díaz (IIS-FJD), 28040 Madrid, Spain
| | - Carmen Ayuso
- CIBERER, Center for Biomedical Research in Rare Diseases Network, 28029 Madrid, Spain; (P.P.); (J.T.-C.); (P.A.); (N.G.-Z.); (A.P.); (L.M.); (M.P.); (E.R.); (F.J.R.); (B.A.); (C.A.); (S.T.S.); (A.I.S.B.); (The SOGRI Consortium); (J.N.)
- Department of Genetics and Genomics, Fundación Jiménez Díaz University Hospital, Health Research Institute Fundación Jiménez Díaz (IIS-FJD), 28040 Madrid, Spain
| | - Saoud Tahsin Swafiri
- CIBERER, Center for Biomedical Research in Rare Diseases Network, 28029 Madrid, Spain; (P.P.); (J.T.-C.); (P.A.); (N.G.-Z.); (A.P.); (L.M.); (M.P.); (E.R.); (F.J.R.); (B.A.); (C.A.); (S.T.S.); (A.I.S.B.); (The SOGRI Consortium); (J.N.)
- Department of Genetics and Genomics, Fundación Jiménez Díaz University Hospital, Health Research Institute Fundación Jiménez Díaz (IIS-FJD), 28040 Madrid, Spain
| | - Ana Isabel Sánchez Barbero
- CIBERER, Center for Biomedical Research in Rare Diseases Network, 28029 Madrid, Spain; (P.P.); (J.T.-C.); (P.A.); (N.G.-Z.); (A.P.); (L.M.); (M.P.); (E.R.); (F.J.R.); (B.A.); (C.A.); (S.T.S.); (A.I.S.B.); (The SOGRI Consortium); (J.N.)
- Department of Genetics and Genomics, Fundación Jiménez Díaz University Hospital, Health Research Institute Fundación Jiménez Díaz (IIS-FJD), 28040 Madrid, Spain
| | - Varunvenkat M. Srinivasan
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore 560029, India; (V.M.S.); (V.K.G.)
| | - Vykuntaraju K. Gowda
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore 560029, India; (V.M.S.); (V.K.G.)
| | - Manuela Morleo
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy; (M.M.); (V.N.)
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Vicenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy; (M.M.); (V.N.)
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Stefano D’Arrigo
- ITHACA, European Reference Network, 1140 Brussels, Belgium; (S.D.); (C.C.)
- Department of Pediatric Neurosciences, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - Claudia Ciaccio
- ITHACA, European Reference Network, 1140 Brussels, Belgium; (S.D.); (C.C.)
- Department of Pediatric Neurosciences, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | | | - Beatriz Paumard
- HM Hospitales, 28660 Madrid, Spain; (C.M.M.); (B.P.); (G.G.)
| | - Gema Guillen
- HM Hospitales, 28660 Madrid, Spain; (C.M.M.); (B.P.); (G.G.)
| | - Ana Teresa Serrano Anton
- Department of Medical Genetics, Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, 30120 Murcia, Spain; (A.T.S.A.); (M.D.J.)
| | - Marta Domínguez Jimenez
- Department of Medical Genetics, Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, 30120 Murcia, Spain; (A.T.S.A.); (M.D.J.)
| | - Veronica Seidel
- Genomics Unit, HGU Gregorio Marañón, 28007 Madrid, Spain; (V.S.); (J.S.)
| | - Julia Suárez
- Genomics Unit, HGU Gregorio Marañón, 28007 Madrid, Spain; (V.S.); (J.S.)
| | - Valerie Cormier-Daire
- Department of Genomic Medicine for Rare Diseases, INSERM UMR1163, Imagine Institute, Necker Enfants Malades Hospital, Paris Cité University, 75015 Paris, France;
| | - The SOGRI Consortium
- CIBERER, Center for Biomedical Research in Rare Diseases Network, 28029 Madrid, Spain; (P.P.); (J.T.-C.); (P.A.); (N.G.-Z.); (A.P.); (L.M.); (M.P.); (E.R.); (F.J.R.); (B.A.); (C.A.); (S.T.S.); (A.I.S.B.); (The SOGRI Consortium); (J.N.)
- INGEMM-IdiPaz, Institute of Medical and Molecular Genetics, 28046 Madrid, Spain; (M.C.); (C.S.)
- ITHACA, European Reference Network, 1140 Brussels, Belgium; (S.D.); (C.C.)
| | - Julián Nevado
- CIBERER, Center for Biomedical Research in Rare Diseases Network, 28029 Madrid, Spain; (P.P.); (J.T.-C.); (P.A.); (N.G.-Z.); (A.P.); (L.M.); (M.P.); (E.R.); (F.J.R.); (B.A.); (C.A.); (S.T.S.); (A.I.S.B.); (The SOGRI Consortium); (J.N.)
- INGEMM-IdiPaz, Institute of Medical and Molecular Genetics, 28046 Madrid, Spain; (M.C.); (C.S.)
- ITHACA, European Reference Network, 1140 Brussels, Belgium; (S.D.); (C.C.)
| | - Pablo Lapunzina
- CIBERER, Center for Biomedical Research in Rare Diseases Network, 28029 Madrid, Spain; (P.P.); (J.T.-C.); (P.A.); (N.G.-Z.); (A.P.); (L.M.); (M.P.); (E.R.); (F.J.R.); (B.A.); (C.A.); (S.T.S.); (A.I.S.B.); (The SOGRI Consortium); (J.N.)
- INGEMM-IdiPaz, Institute of Medical and Molecular Genetics, 28046 Madrid, Spain; (M.C.); (C.S.)
- ITHACA, European Reference Network, 1140 Brussels, Belgium; (S.D.); (C.C.)
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