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Treccarichi S, Calì F, Vinci M, Ragalmuto A, Musumeci A, Federico C, Costanza C, Bottitta M, Greco D, Saccone S, Elia M. Implications of a De Novo Variant in the SOX12 Gene in a Patient with Generalized Epilepsy, Intellectual Disability, and Childhood Emotional Behavioral Disorders. Curr Issues Mol Biol 2024; 46:6407-6422. [PMID: 39057025 PMCID: PMC11276073 DOI: 10.3390/cimb46070383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/17/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
SRY-box transcription factor (SOX) genes, a recently discovered gene family, play crucial roles in the regulation of neuronal stem cell proliferation and glial differentiation during nervous system development and neurogenesis. Whole exome sequencing (WES) in patients presenting with generalized epilepsy, intellectual disability, and childhood emotional behavioral disorder, uncovered a de novo variation within SOX12 gene. Notably, this gene has never been associated with neurodevelopmental disorders. No variants in known genes linked with the patient's symptoms have been detected by the WES Trio analysis. To date, any MIM phenotype number associated with intellectual developmental disorder has not been assigned for SOX12. In contrast, both SOX4 and SOX11 genes within the same C group (SoxC) of the Sox gene family have been associated with neurodevelopmental disorders. The variant identified in the patient here described was situated within the critical high-mobility group (HMG) functional site of the SOX12 protein. This domain, in the Sox protein family, is essential for DNA binding and bending, as well as being responsible for transcriptional activation or repression during the early stages of gene expression. Sequence alignment within SoxC (SOX12, SOX4 and SOX11) revealed a high conservation rate of the HMG region. The in silico predictive analysis described this novel variant as likely pathogenic. Furthermore, the mutated protein structure predictions unveiled notable changes with potential deleterious effects on the protein structure. The aim of this study is to establish a correlation between the SOX12 gene and the symptoms diagnosed in the patient.
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Affiliation(s)
- Simone Treccarichi
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (S.T.); (F.C.); (M.V.); (A.R.); (A.M.); (M.B.); (D.G.); (M.E.)
| | - Francesco Calì
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (S.T.); (F.C.); (M.V.); (A.R.); (A.M.); (M.B.); (D.G.); (M.E.)
| | - Mirella Vinci
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (S.T.); (F.C.); (M.V.); (A.R.); (A.M.); (M.B.); (D.G.); (M.E.)
| | - Alda Ragalmuto
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (S.T.); (F.C.); (M.V.); (A.R.); (A.M.); (M.B.); (D.G.); (M.E.)
| | - Antonino Musumeci
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (S.T.); (F.C.); (M.V.); (A.R.); (A.M.); (M.B.); (D.G.); (M.E.)
| | - Concetta Federico
- Department of Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy;
| | - Carola Costanza
- Department of Sciences for Health Promotion and Mother and Child Care “G. D’Alessandro”, University of Palermo, 90128 Palermo, Italy;
| | - Maria Bottitta
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (S.T.); (F.C.); (M.V.); (A.R.); (A.M.); (M.B.); (D.G.); (M.E.)
| | - Donatella Greco
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (S.T.); (F.C.); (M.V.); (A.R.); (A.M.); (M.B.); (D.G.); (M.E.)
| | - Salvatore Saccone
- Department of Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy;
| | - Maurizio Elia
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (S.T.); (F.C.); (M.V.); (A.R.); (A.M.); (M.B.); (D.G.); (M.E.)
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Vetri L, Calì F, Saccone S, Vinci M, Chiavetta NV, Carotenuto M, Roccella M, Costanza C, Elia M. Whole Exome Sequencing as a First-Line Molecular Genetic Test in Developmental and Epileptic Encephalopathies. Int J Mol Sci 2024; 25:1146. [PMID: 38256219 PMCID: PMC10816140 DOI: 10.3390/ijms25021146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/11/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
Developmental and epileptic encephalopathies (DEE) are severe neurodevelopmental disorders characterized by recurrent, usually early-onset, epileptic seizures accompanied by developmental impairment often related to both underlying genetic etiology and abnormal epileptiform activity. Today, next-generation sequencing technologies (NGS) allow us to sequence large portions of DNA quickly and with low costs. The aim of this study is to evaluate the use of whole-exome sequencing (WES) as a first-line molecular genetic test in a sample of subjects with DEEs characterized by early-onset drug-resistant epilepsies, associated with global developmental delay and/or intellectual disability (ID). We performed 82 WESs, identifying 35 pathogenic variants with a detection rate of 43%. The identified variants were highlighted on 29 different genes including, 3 new candidate genes (KCNC2, STXBP6, DHRS9) for DEEs never identified before. In total, 23 out of 35 (66%) de novo variants were identified. The most frequently identified type of inheritance was autosomal dominant de novo (60%) followed by autosomal recessive in homozygosity (17%) and heterozygosity (11%), autosomal dominant inherited from parental mosaicism (6%) and X-linked dominant de novo (6%). The most frequent mutations identified were missense (75%) followed by frameshift deletions (16%), frameshift duplications (5%), and splicing mutations (3%). Considering the results obtained in the present study we support the use of WES as a form of first-line molecular genetic testing in DEEs.
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Affiliation(s)
- Luigi Vetri
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (L.V.); (M.V.); (N.V.C.); (M.E.)
| | - Francesco Calì
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (L.V.); (M.V.); (N.V.C.); (M.E.)
| | - Salvatore Saccone
- Department Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy
| | - Mirella Vinci
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (L.V.); (M.V.); (N.V.C.); (M.E.)
| | | | - Marco Carotenuto
- Clinic of Child and Adolescent Neuropsychiatry, Department of Mental Health, Physical and Preventive Medicine, University of Campania “Luigi Vanvitelli”, 80131 Naples, Italy;
| | - Michele Roccella
- Department of Psychology, Educational Science and Human Movement, University of Palermo, 90141 Palermo, Italy; (M.R.); (C.C.)
| | - Carola Costanza
- Department of Psychology, Educational Science and Human Movement, University of Palermo, 90141 Palermo, Italy; (M.R.); (C.C.)
| | - Maurizio Elia
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (L.V.); (M.V.); (N.V.C.); (M.E.)
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