{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T16:54:12Z","timestamp":1785430452329,"version":"3.56.0"},"reference-count":42,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T00:00:00Z","timestamp":1780444800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"publisher","award":["PNRR-MR1-2023-12377843"],"award-info":[{"award-number":["PNRR-MR1-2023-12377843"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"award":["PNRR-MR1-2023-12377843"],"award-info":[{"award-number":["PNRR-MR1-2023-12377843"]}],"id":[{"id":"https:\/\/ror.org\/019w4f821","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background: Autosomal recessive intellectual developmental disorder-13 (MRT13; OMIM #613192) is a rare neurodevelopmental disorder caused by pathogenic variants in TRAPPC9. Most reported variants are single-nucleotide variants (SNVs), small insertions\/deletions, or copy number variants (CNVs), whereas complex structural variants (SVs) remain poorly characterized. Objectives: This study sought to review the clinical and molecular spectrum of TRAPPC9-related disorder, harmonize reported variants, explore genotype\u2013phenotype correlations, and expand the mutational spectrum by reporting a novel patient with a cryptic SV. Methods: We report a novel patient whose diagnostic workup included array-CGH, whole-exome sequencing, karyotyping, and optical genome mapping. Additionally, a systematic literature search was primarily conducted in PubMed\/MEDLINE from 2009 to January 2026, with Embase, Web of Science, Google Scholar, Orphanet, OMIM, and ClinVar used as supplementary sources. Patients carrying pathogenic\/likely pathogenic TRAPPC9 variants were included. Clinical and molecular data were extracted and descriptively summarized. Genotype\u2013phenotype correlations were explored. Reported variants were re-annotated using MANE Select reference transcripts. Results: The reported patient showed biallelic TRAPPC9 disruption due to two independently inherited structural variants: a maternal ~35 kb intragenic deletion involving exons 10\u201312, identified by 400K array-CGH, and a paternal balanced translocation t(4;8) disrupting TRAPPC9 within intron 8, characterized by trio-OGM and paired-end whole-genome sequencing (PE-WGS). Thirty-one studies reporting 75 previously published patients were included in the literature review; together with the novel patient described here, the final cohort comprised 76 patients. Intellectual disability was present in 100% of cases, followed by brain MRI abnormalities (95.9%), microcephaly (82.3%), motor delay (71.4%), dysmorphic features (69.8%), obesity (52.8%), behavioral abnormalities\/autism spectrum disorder (49.2%\/43.8%), and epilepsy (15.9%). Most patients (84.2%) harbored homozygous variants. Thirty-two distinct sequence variants were identified, predominantly loss-of-function. CNVs were identified in 13.2% of patients. No genotype\u2013phenotype correlations were identified. Conclusions: The systematic review provides an updated and harmonized overview of the clinical and molecular spectrum of TRAPPC9-related disorder, supporting the presence of a recognizable phenotype and confirming the predominance of loss-of-function variants. Our case further highlights the contribution of cryptic structural variants to the mutational spectrum of TRAPPC9 and the diagnostic value of advanced genomic approaches.<\/jats:p>","DOI":"10.3390\/genes17060658","type":"journal-article","created":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T18:08:07Z","timestamp":1780510087000},"page":"658","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["TRAPPC9-Related Intellectual Developmental Disorder: A Systematic Review and a Novel Case of a Complex Structural Variant"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-7207-6784","authenticated-orcid":false,"given":"Marta","family":"Calvo","sequence":"first","affiliation":[{"name":"Department of Public Health and Pediatrics, University of Turin, 10126 Turin, Italy"},{"name":"Postgraduate School of Pediatrics, Department of Public Health and Pediatrics, University of Turin, 10126 Turin, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0447-2112","authenticated-orcid":false,"given":"Giuseppe","family":"Reynolds","sequence":"additional","affiliation":[{"name":"Department of Public Health and Pediatrics, University of Turin, 10126 Turin, Italy"},{"name":"Postgraduate School of Pediatrics, Department of Public Health and Pediatrics, University of Turin, 10126 Turin, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-1239-0829","authenticated-orcid":false,"given":"Maria","family":"Luca","sequence":"additional","affiliation":[{"name":"Pediatric Clinical Genetics, Regina Margherita Children\u2019s Hospital, 10126 Turin, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eleonora","family":"Di Gregorio","sequence":"additional","affiliation":[{"name":"Medical Genetics Unit, Citt\u00e0 della Salute e della Scienza University Hospital, 10126 Turin, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8927-8900","authenticated-orcid":false,"given":"Simona","family":"Cardaropoli","sequence":"additional","affiliation":[{"name":"Department of Public Health and Pediatrics, University of Turin, 10126 Turin, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9407-3195","authenticated-orcid":false,"given":"Eliana","family":"Salvo","sequence":"additional","affiliation":[{"name":"Cytogenetics Laboratory, Scientific Institute, IRCCS Eugenio Medea, 23849\u00a0Lecco, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-0859-4036","authenticated-orcid":false,"given":"Ilaria","family":"Carelli","sequence":"additional","affiliation":[{"name":"Department of Medical Sciences, University of Turin, 10126 Turin, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3162-9771","authenticated-orcid":false,"given":"Federico","family":"Rondot","sequence":"additional","affiliation":[{"name":"Department of Public Health and Pediatrics, University of Turin, 10126 Turin, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-4679-2982","authenticated-orcid":false,"given":"Stefania","family":"Massuras","sequence":"additional","affiliation":[{"name":"Pediatric Clinical Genetics, Regina Margherita Children\u2019s Hospital, 10126 Turin, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5690-6504","authenticated-orcid":false,"given":"Diana","family":"Carli","sequence":"additional","affiliation":[{"name":"Pediatric Clinical Genetics, Regina Margherita Children\u2019s Hospital, 10126 Turin, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-2737-7420","authenticated-orcid":false,"given":"Roberta","family":"Marinoni","sequence":"additional","affiliation":[{"name":"Medical Genetics Unit, Citt\u00e0 della Salute e della Scienza University Hospital, 10126 Turin, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7121-7712","authenticated-orcid":false,"given":"Maria Clara","family":"Bonaglia","sequence":"additional","affiliation":[{"name":"Cytogenetics Laboratory, Scientific Institute, IRCCS Eugenio Medea, 23849\u00a0Lecco, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alessandro","family":"Mussa","sequence":"additional","affiliation":[{"name":"Department of Public Health and Pediatrics, University of Turin, 10126 Turin, Italy"},{"name":"Pediatric Clinical Genetics, Regina Margherita Children\u2019s Hospital, 10126 Turin, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,3]]},"reference":[{"key":"ref_1","first-page":"2991","article-title":"TRAPPC9: Novel insights into its trafficking and signaling pathways in health and disease (Review)","volume":"42","author":"Mbimba","year":"2018","journal-title":"Int. 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