Exome study of single nucleotide variations in patients with syndromic and non-syndromic autism reveals potential candidate genes for diagnostics and novel single nucleotide variants
Open accessAbstract
Autism spectrum disorder (ASD) is a neurodevelopmental impairment that occurs due to mutations related to the formation of the nervous system, combined with the impact of various epigenetic and environmental factors. This necessitates the identification of the genetic variations involved in ASD pathogenesis. We performed whole exome sequencing (WES) in a cohort of 22 Bulgarian male and female individuals showing ASD features alongside segregation analyses of their families. A targeted panel of genes was chosen and analyzed for each case, based on a detailed examination of clinical data. Gene analyses revealed that specific variants concern key neurobiological processes involving neuronal architecture, development, and function. These variants occur in a number of genes, including SHANK3, DLG3, NALCN, and PACS2 which are critical for synaptic signaling imbalance, CEP120 and BBS5 for ciliopathies, SPTAN1 for spectrins structure, SPATA5, TRAK1, and VPS13B for neuronal organelles trafficking and integrity, TAF6, SMARCB1, DDX3X, MECP2, and SETD1A for gene expression, CDK13 for cell cycle control, ALDH5A1, DPYD, FH, and PDHX for mitochondrial function, and PQBP1, HUWE1, and WDR45 for neuron homeostasis. Novel single nucleotide variants in the SPATA5, CEP120, BBS5, SETD1A, TRAK1, VPS13B, and DDX3X genes have been identified and proposed for use in ASD diagnostics. Our data contribute to a better understanding of the complex neurobiological features of autism and are applicable in the diagnosis and development of personalized therapeutic approaches.
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In non-syndromic ASD, SHANK3 mutations primarily manifest as direct disruptions to synaptic architecture and function without consistent extra-neurological anomalies.
“In non-syndromic ASD, SHANK3 mutations primarily manifest as direct disruptions to synaptic architecture and function without consistent extra-neurological anomalies (Hamoudi et al., 2022; Belenska-Todorova et al., 2025).”
From Biological hierarchy from genotype to phenotype in syndromic and non-syndromic autism spectrum disorder (2026) · cites this paper as Belenska-Todorova et al., 2025
Discussion §4.1 reports a SHANK3 variant in a patient with ASD and says it may disrupt synaptic function; the Conclusions also link ASD-associated mutations to synaptic architecture. The paper does not establish that SHANK3 mutations primarily have this effect in non-syndromic ASD or that they lack consistent extra-neurological anomalies. Its SHANK3 case also carries a DLG3 variant. (LLM, conf=0.86)
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The continuously evolving phenotype of succinic semialdehyde dehydrogenase deficiency
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Shank3 deficiency elicits autistic-like behaviors by activating p38α in hypothalamic AgRP neurons
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Succinic Semialdehyde Dehydrogenase Deficiency Presenting as Autism Spectrum Disorder
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Flagged first, then by citations
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DDX3X Sendromu ve Eşlik Eden Otizm Spektrum Bozukluğu Olan Kız Çocuk: Bir Olgu Sunumu
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Molecular Mechanisms of Autism Spectrum Disorder
Gandhi, T., & Lee, C. C. (2026) · Cells · doi:10.3390/cells15080688
- Authors
- Belenska-Todorova, L., Zamfirov, M., Todorov, T., Atemin, S., Sleptsova, M., Pavlova, Z., Kadiyska, T., Maver, A., Peterlin, B., & Todorova, A.
- Affiliations
- Sofia University "St. Kliment Ohridski" (BG)
- Genetic Medico-Diagnostic Laboratory Genica, 1000 Sofia, Bulgaria
- Independent Medico-Diagnostic Laboratory Genome Center “Bulgaria”, 1000 Sofia, Bulgaria
- Medical University of Sofia (BG)
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Ljubljana University Medical Centre (SI)
- Corresponding author
- Belenska-Todorova, Lyudmila
- ORCID
- Venue
- Cells
- Publisher
- MDPI AG
- Published
- 2025-06-17
- Volume
- 14
- Issue
- 12
- Pages
- 915
- ISSN
- 2073-4409 (ISSN-L)
- PMC
- PMC12191266
- OpenAlex
- W4411367483
- Cited by
- 5
- References
- 93
- Citations by year
- 2026: 5
- FWCI
- 2.85
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Cells (publishedVersion, cc-by)
- Preprints.org (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- European Union-NextGenerationEU
- Topics
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- autism spectrum disorder, single nucleotide variants, syndromic autism, non-syndromic autism, candidate genes, novel variants, SHANK3, DLG3, NALCN, ciliopathies, BBS5, SPTAN1, spectrin, TRAK1, VPS13B, MeCP2, SETD1A, mitochondrial function, SMARCB1, DDX3X, CDK13, cell cycle regulation, segregation analysis
- MeSH terms
- Autism Spectrum Disorder, Exome Sequencing, Adolescent, Adult, Autistic Disorder, Child, Child, Preschool, Female, Humans, Male, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Genetic Association Studies, Exome
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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