{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,3]],"date-time":"2026-11-03T04:02:24Z","timestamp":1793678544433,"version":"4.5.1"},"reference-count":40,"publisher":"MDPI AG","issue":"15","license":[{"start":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T00:00:00Z","timestamp":1785542400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100015550","name":"Italian Ministry of Health","doi-asserted-by":"publisher","award":["CCR-2017-9999901"],"award-info":[{"award-number":["CCR-2017-9999901"]}],"id":[{"id":"10.13039\/501100015550","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Autism spectrum disorder (ASD) is genetically heterogeneous, involving rare and common variants that disrupt neurodevelopmental pathways. To explore this complexity, we performed whole-exome sequencing in children with ASD. Clinical phenotypes were systematically recorded, and severity was classified according to DSM-5 criteria. Variants were interpreted using ACMG guidelines, with recurrence analysis to identify genes shared across individuals and cohort enrichment testing against gnomAD. To examine genotype-phenotype relationships, we applied SKAT\/SKAT-O across 16 phenotypes after covariate adjustment. Among 25 included individuals, pathogenic or likely pathogenic variants were found in 9, yielding a diagnostic yield of 36%. These involved genes linked to neurodevelopmental, epileptic, metabolic, and syndromic disorders. Recurrence analysis identified 586 genes present in at least two individuals, with PABPC1, GTF2I, PCLO, PKD1, and EP400 being the most frequent. SKAT\/SKAT-O revealed the strongest burden associations for motor delay, aggressive behavior, mutism, anxiety, unresponsiveness to spoken voice, digestive disorder, and sleep disturbances, with limited overlap across phenotypes. Several recurrent genes also showed phenotype-specific associations. Overall, this integrative WES study provides clinically actionable diagnoses, highlights recurrent genes, and uncovers phenotype-specific signals, supporting convergent pathways with gene-level heterogeneity.<\/jats:p>","DOI":"10.3390\/ijms27156901","type":"journal-article","created":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T12:57:56Z","timestamp":1785761876000},"page":"6901","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Genetic Heterogeneity in Autism Spectrum Disorder: Diagnostic Yield, Recurrent Genes, and Rare Variant-Phenotype Associations from Whole-Exome Sequencing"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-9167-5228","authenticated-orcid":false,"given":"Zainab","family":"Gaouzi","sequence":"first","affiliation":[{"name":"Mohammed VI University of Sciences and Health (UM6SS), Casablanca 82403, Morocco"},{"name":"Mohammed VI Center for Research and Innovation (CM6RI), Rabat 10100, Morocco"},{"name":"Department of Clinical and Experimental Medicine, University of Messina, 98122 Messina, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-6714-6952","authenticated-orcid":false,"given":"Giulia","family":"Spoto","sequence":"additional","affiliation":[{"name":"Unit of Child Neurology and Psychiatry, Department BIOMORF, University Hospital of Messina, 98125 Messina, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4594-2651","authenticated-orcid":false,"given":"Francesca","family":"Polito","sequence":"additional","affiliation":[{"name":"Department of Clinical and Experimental Medicine, University of Messina, 98122 Messina, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rihab","family":"Festali","sequence":"additional","affiliation":[{"name":"Mohammed VI University of Sciences and Health (UM6SS), Casablanca 82403, Morocco"},{"name":"Mohammed VI Center for Research and Innovation (CM6RI), Rabat 10100, Morocco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Irene","family":"Gasparo","sequence":"additional","affiliation":[{"name":"Department of Clinical and Experimental Medicine, University of Messina, 98122 Messina, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Licitri","sequence":"additional","affiliation":[{"name":"Department of Clinical and Experimental Medicine, University of Messina, 98122 Messina, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna Maria","family":"Mirabello","sequence":"additional","affiliation":[{"name":"Department of Clinical and Experimental Medicine, University of Messina, 98122 Messina, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvia","family":"Romano","sequence":"additional","affiliation":[{"name":"Department of Clinical and Experimental Medicine, University of Messina, 98122 Messina, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vincenzo","family":"Macaione","sequence":"additional","affiliation":[{"name":"Department of Clinical and Experimental Medicine, University of Messina, 98122 Messina, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nouzha","family":"Dini","sequence":"additional","affiliation":[{"name":"Mohammed VI University of Sciences and Health (UM6SS), Casablanca 82403, Morocco"},{"name":"Sheikh Khalifa International University Hospital, Faculty of Medicine, Mohammed VI University of Health Sciences, Casablanca 82403, Morocco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7812-0641","authenticated-orcid":false,"given":"Elmostafa","family":"El Fahime","sequence":"additional","affiliation":[{"name":"Mohammed VI University of Sciences and Health (UM6SS), Casablanca 82403, Morocco"},{"name":"Mohammed VI Center for Research and Innovation (CM6RI), Rabat 10100, Morocco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saber","family":"Boutayeb","sequence":"additional","affiliation":[{"name":"Mohammed VI University of Sciences and Health (UM6SS), Casablanca 82403, Morocco"},{"name":"Mohammed VI Center for Research and Innovation (CM6RI), Rabat 10100, Morocco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yamna","family":"Kriouile","sequence":"additional","affiliation":[{"name":"Faculty of Medicine and Pharmacy, Rabat University of Mohammed V Rabat, Rabat 11000, Morocco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4122-2294","authenticated-orcid":false,"given":"Idrissa","family":"Diawara","sequence":"additional","affiliation":[{"name":"Mohammed VI University of Sciences and Health (UM6SS), Casablanca 82403, Morocco"},{"name":"Mohammed VI Center for Research and Innovation (CM6RI), Rabat 10100, Morocco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriella","family":"di Rosa","sequence":"additional","affiliation":[{"name":"Unit of Child Neurology and Psychiatry, Department BIOMORF, University Hospital of Messina, 98125 Messina, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mhammed","family":"Aguennouz","sequence":"additional","affiliation":[{"name":"Department of Clinical and Experimental Medicine, University of Messina, 98122 Messina, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,1]]},"reference":[{"key":"ref_1","unstructured":"Essa, M.M., and Qoronfleh, M.W. (2020). Neuropsychopathology of Autism Spectrum Disorder: Complex Interplay of Genetic, Epigenetic, and Environmental Factors. Personalized Food Intervention and Therapy for Autism Spectrum Disorder Management [Internet], Springer International Publishing."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1007\/s00702-023-02595-9","article-title":"Autism Spectrum Disorder and auditory sensory alterations: A systematic review on the integrity of cognitive and neuronal functions related to auditory processing","volume":"130","author":"Monteiro","year":"2023","journal-title":"J. Neural Transm."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1038\/s41583-022-00576-7","article-title":"Genomics, convergent neuroscience and progress in understanding autism spectrum disorder","volume":"23","author":"Willsey","year":"2022","journal-title":"Nat. Rev. Neurosci."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1038\/nrn3992","article-title":"From the genetic architecture to synaptic plasticity in autism spectrum disorder","volume":"16","author":"Bourgeron","year":"2025","journal-title":"Nat. Rev. Neurosci."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Sheth, F., Shah, J., Jain, D., Shah, S., Patel, H., Patel, K., I Solanki, D., Iyer, A.S., Menghani, B., and Mhatre, P. (2023). Comparative yield of molecular diagnostic algorithms for autism spectrum disorder diagnosis in India: Evidence supporting whole exome sequencing as first tier test. BMC Neurol., 23.","DOI":"10.1186\/s12883-023-03341-0"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Mellone, S., Puricelli, C., Vurchio, D., Ronzani, S., Favini, S., Maruzzi, A., Peruzzi, C., Papa, A., Spano, A., and Sirchia, F. (2022). The Usefulness of a Targeted Next Generation Sequencing Gene Panel in Providing Molecular Diagnosis to Patients With a Broad Spectrum of Neurodevelopmental Disorders. Front. Genet., 13.","DOI":"10.3389\/fgene.2022.875182"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1186\/s13023-024-03214-w","article-title":"Phenotypic and genetic analysis of children with unexplained neurodevelopmental delay and neurodevelopmental comorbidities in a Chinese cohort using trio-based whole-exome sequencing","volume":"19","author":"Wu","year":"2024","journal-title":"Orphanet J. Rare Dis."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2413","DOI":"10.1038\/s41436-019-0554-6","article-title":"Meta-analysis and multidisciplinary consensus statement: Exome sequencing is a first-tier clinical diagnostic test for individuals with neurodevelopmental disorders","volume":"21","author":"Srivastava","year":"2019","journal-title":"Genet. Med."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Qi, Y., Wang, M., and Jiang, Q. (2022). PABPC1\u2014mRNA stability, protein translation and tumorigenesis. Front. Oncol., 12.","DOI":"10.3389\/fonc.2022.1025291"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1186\/s13229-020-00386-7","article-title":"De novo missense variants disrupting protein\u2013protein interactions affect risk for autism through gene co-expression and protein networks in neuronal cell types","volume":"11","author":"Chen","year":"2020","journal-title":"Mol. Autism"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1459","DOI":"10.1007\/s10803-011-1389-4","article-title":"Association of GTF2i in the Williams-Beuren Syndrome Critical Region with Autism Spectrum Disorders","volume":"42","author":"Malenfant","year":"2012","journal-title":"J. Autism Dev. Disord."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"103795","DOI":"10.1016\/j.mcn.2022.103795","article-title":"Synaptic logistics: The presynaptic scaffold protein Piccolo a nodal point tuning synaptic vesicle recycling, maintenance and integrity","volume":"124","author":"Garner","year":"2023","journal-title":"Mol. Cell. Neurosci."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/j.ajhg.2024.11.010","article-title":"Variants in EP400, encoding a chromatin remodeler, cause epilepsy with neurodevelopmental disorders","volume":"112","author":"Luo","year":"2025","journal-title":"Am. J. Hum. Genet."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2517","DOI":"10.1007\/s00018-020-03714-5","article-title":"The emerging role of chromatin remodelers in neurodevelopmental disorders: A developmental perspective","volume":"78","author":"Mossink","year":"2021","journal-title":"Cell. Mol. Life Sci."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1300","DOI":"10.1038\/ng.2765","article-title":"Mutations in genes encoding the cadherin receptor-ligand pair DCHS1 and FAT4 disrupt cerebral cortical development","volume":"45","author":"Cappello","year":"2013","journal-title":"Nat. Genet."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Mu\u00f1oz-Lasso, D.C., Rom\u00e1-Mateo, C., Pallard\u00f3, F.V., and Gonzalez-Cabo, P. (2020). Much More Than a Scaffold: Cytoskeletal Proteins in Neurological Disorders. Cells, 9.","DOI":"10.3390\/cells9020358"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1016\/j.ajhg.2012.06.007","article-title":"Optimal Unified Approach for Rare-Variant Association Testing with Application to Small-Sample Case-Control Whole-Exome Sequencing Studies","volume":"91","author":"Lee","year":"2012","journal-title":"Am. J. Hum. Genet."},{"key":"ref_18","unstructured":"Madranges, J.F. (2026). Neuronal Axon Guidance Cue in Neurodevelopment, Maturation and Plasticity [Internet], McGill University. Available online: https:\/\/escholarship.mcgill.ca\/concern\/theses\/m900p128k."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1038\/cdd.2011.121","article-title":"Fas death receptor signalling: Roles of Bid and XIAP","volume":"19","author":"Kaufmann","year":"2012","journal-title":"Cell Death Differ."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"2225","DOI":"10.1016\/j.celrep.2018.04.054","article-title":"Molecular and Functional Sex Differences of Noradrenergic Neurons in the Mouse Locus Coeruleus","volume":"23","author":"Mulvey","year":"2018","journal-title":"Cell Rep."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"3051","DOI":"10.1007\/s00018-018-2779-y","article-title":"Degradation of the mitochondrial complex I assembly factor TMEM126B under chronic hypoxia","volume":"75","author":"Fuhrmann","year":"2026","journal-title":"Cell. Mol. Life Sci."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1038\/s41586-025-10047-5","article-title":"Developmental convergence and divergence in human stem cell models of autism","volume":"651","author":"Gordon","year":"2026","journal-title":"Nature"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Khoja, S., Haile, M.T., and Chen, L.Y. (2023). Advances in neurexin studies and the emerging role of neurexin-2 in autism spectrum disorder. Front. Mol. Neurosci., 16.","DOI":"10.3389\/fnmol.2023.1125087"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"568","DOI":"10.1016\/j.cell.2019.12.036","article-title":"Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism","volume":"180","author":"Satterstrom","year":"2020","journal-title":"Cell"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1320","DOI":"10.1038\/s41588-022-01104-0","article-title":"Rare coding variation provides insight into the genetic architecture and phenotypic context of autism","volume":"54","author":"Fu","year":"2022","journal-title":"Nat. Genet."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1305","DOI":"10.1038\/s41588-022-01148-2","article-title":"Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes","volume":"54","author":"Zhou","year":"2022","journal-title":"Nat. Genet."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1293","DOI":"10.1038\/s41588-022-01072-5","article-title":"Genetic correlates of phenotypic heterogeneity in autism","volume":"54","author":"Warrier","year":"2022","journal-title":"Nat. Genet."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1284","DOI":"10.1038\/s41588-022-01064-5","article-title":"A phenotypic spectrum of autism is attributable to the combined effects of rare variants, polygenic risk and sex","volume":"54","author":"Antaki","year":"2022","journal-title":"Nat. Genet."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"e2148","DOI":"10.1002\/mgg3.2148","article-title":"The current benefit of genome sequencing compared to exome sequencing in patients with developmental or epileptic encephalopathies","volume":"11","author":"Grether","year":"2023","journal-title":"Mol. Genet. Genom. Med."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"103126","DOI":"10.1016\/j.gimo.2025.103126","article-title":"P757: Validation and implementation of Emedgene variant interpretation and reporting software for clinical genomic testing","volume":"3","author":"Qiao","year":"2025","journal-title":"Genet. Med. Open"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Scheffler, K., Catreux, S., O\u2019Connell, T., Jo, H., Jain, V., and Heyns, T. (2023). Somatic small-variant calling methods in Illumina DRAGENTM Secondary Analysis. bioRxiv, 2023.03.23.534011.","DOI":"10.1101\/2023.03.23.534011"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"D789","DOI":"10.1093\/nar\/gku1205","article-title":"OMIM.org: Online Mendelian Inheritance in Man (OMIM\u00ae), an online catalog of human genes and genetic disorders","volume":"43","author":"Amberger","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Pavan, S., Rommel, K., Marquina, M.E.M., H\u00f6hn, S., Lanneau, V., and Rath, A. (2017). Clinical Practice Guidelines for Rare Diseases: The Orphanet Database. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0170365"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"D980","DOI":"10.1093\/nar\/gkt1113","article-title":"ClinVar: Public archive of relationships among sequence variation and human phenotype","volume":"42","author":"Landrum","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1038\/gim.2015.30","article-title":"Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology","volume":"17","author":"Richards","year":"2015","journal-title":"Genet. Med."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1242\/dmm.005439","article-title":"SFARI Gene: An evolving database for the autism research community","volume":"3","author":"Packer","year":"2010","journal-title":"Dis. Models Mech."},{"key":"ref_37","unstructured":"Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv."},{"key":"ref_38","first-page":"11.10.1","article-title":"From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline","volume":"43","author":"Carneiro","year":"2013","journal-title":"Curr. Protoc. Bioinform."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1093\/nar\/29.1.308","article-title":"DbSNP: The NCBI database of genetic variation","volume":"29","author":"Sherry","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"e164","DOI":"10.1093\/nar\/gkq603","article-title":"ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/15\/6901\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,10]],"date-time":"2026-08-10T09:25:32Z","timestamp":1786353932000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/15\/6901"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,1]]},"references-count":40,"journal-issue":{"issue":"15","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["ijms27156901"],"URL":"https:\/\/doi.org\/10.3390\/ijms27156901","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,1]]}}}