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Its characteristic features\u2014generalized hypertrichosis, coarse facial appearance, skeletal abnormalities, and cardiovascular involvement\u2014may be overlooked when other major comorbidities dominate the clinical picture. Case Presentation: A 29-year-old Taiwanese woman, born prematurely and complicated by neonatal hydrocephalus with subdural hemorrhage requiring ventriculoperitoneal shunt placement, had been followed since infancy under a working diagnosis of cerebral palsy with left hemiparesis and borderline-to-mild intellectual disability. Over the ensuing years, additional features gradually emerged, including generalized hypertrichosis with thick scalp and body hair, coarse facial features, bilateral hallux valgus, mild thoracic scoliosis, polycystic ovaries, mild aortic regurgitation, recurrent hemoptysis associated with abnormal pulmonary vasculature, and iron-deficiency anemia. Earlier genetic investigations\u2014including chromosome analysis (46,XX), array comparative genomic hybridization (array-CGH; 2013), and a trio-based next-generation sequencing study performed under a national rare disease research initiative (2019)\u2014were unrevealing. Whole-genome sequencing performed in December 2025 identified a heterozygous ABCC9 variant (NM_020297.4:c.4174A&gt;G, p.(Ile1392Val)), initially classified as a variant of uncertain significance. Parental Sanger sequencing confirmed the variant to be de novo, and reclassification according to ACMG\/AMP criteria supported a likely pathogenic interpretation. Re-evaluation of the patient\u2019s phenotype demonstrated findings consistent with Cant\u00fa syndrome. Conclusions: This case illustrates how Cant\u00fa syndrome may remain unrecognized for years when a prominent neurological comorbidity\u2014perinatally acquired hydrocephalus and presumed cerebral palsy\u2014dominates the clinical narrative. We report a previously undescribed de novo ABCC9 missense variant (c.4174A&gt;G, p.(Ile1392Val)), thereby expanding the mutational spectrum associated with Cant\u00fa syndrome. This case also highlights the practical value of resequencing and periodic reanalysis using updated next-generation sequencing platforms in patients with long-standing undiagnosed disease, even after prior negative genetic testing.<\/jats:p>","DOI":"10.3390\/diagnostics16142204","type":"journal-article","created":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T05:39:38Z","timestamp":1784093978000},"page":"2204","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["From Array-CGH to Whole-Genome Sequencing: A 29-Year Diagnostic Journey Culminating in the Identification of a De Novo ABCC9 Variant Consistent with Cant\u00fa Syndrome"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8178-6938","authenticated-orcid":false,"given":"Chung-Lin","family":"Lee","sequence":"first","affiliation":[{"name":"Department of Pediatrics, MacKay Memorial Hospital, Taipei 104217, Taiwan"},{"name":"Institute of Clinical Medicine, National Yang-Ming Chiao-Tung University, Taipei 112304, Taiwan"},{"name":"International Rare Disease Center, MacKay Memorial Hospital, Taipei 104217, Taiwan"},{"name":"Department of Medicine, MacKay Medical University, New Taipei City 252005, Taiwan"},{"name":"Department of Nursing, MacKay Junior College of Medicine, Nursing and Management, New Taipei City 252005, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ya-Hui","family":"Chang","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, MacKay Memorial Hospital, Taipei 104217, Taiwan"},{"name":"International Rare Disease Center, MacKay Memorial Hospital, Taipei 104217, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9776-2092","authenticated-orcid":false,"given":"Chih-Kuang","family":"Chuang","sequence":"additional","affiliation":[{"name":"Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei 104217, Taiwan"},{"name":"College of Medicine, Fu-Jen Catholic University, New Taipei City 242062, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huei-Ching","family":"Chiu","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, MacKay Memorial Hospital, Taipei 104217, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan-Rong","family":"Tu","sequence":"additional","affiliation":[{"name":"Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei 104217, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yun-Ting","family":"Lo","sequence":"additional","affiliation":[{"name":"International Rare Disease Center, MacKay Memorial Hospital, Taipei 104217, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun-Yi","family":"Wu","sequence":"additional","affiliation":[{"name":"International Rare Disease Center, MacKay Memorial Hospital, Taipei 104217, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9619-0990","authenticated-orcid":false,"given":"Hsiang-Yu","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, MacKay Memorial Hospital, Taipei 104217, Taiwan"},{"name":"International Rare Disease Center, MacKay Memorial Hospital, Taipei 104217, Taiwan"},{"name":"Department of Medicine, MacKay Medical University, New Taipei City 252005, Taiwan"},{"name":"Department of Nursing, MacKay Junior College of Medicine, Nursing and Management, New Taipei City 252005, Taiwan"},{"name":"Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei 104217, Taiwan"},{"name":"Department of Medical Research, China Medical University Hospital, Taichung 404327, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuan-Pei","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, MacKay Memorial Hospital, Taipei 104217, Taiwan"},{"name":"International Rare Disease Center, MacKay Memorial Hospital, Taipei 104217, Taiwan"},{"name":"Department of Medicine, MacKay Medical University, New Taipei City 252005, Taiwan"},{"name":"Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei 104217, Taiwan"},{"name":"Department of Infant and Child Care, National Taipei University of Nursing and Health Sciences, Taipei 112303, Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1007\/BF00281261","article-title":"A distinct osteochondrodysplasia with hypertrichosis\u2014Individualization of a probable autosomal recessive entity","volume":"60","year":"1982","journal-title":"Hum. 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