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These copy number variants\u00a0are primarily mediated by nonallelic homologous recombination (NAHR) leading to recurrent tandem duplications and reciprocal deletions of the genomic interval mapping between the repeats. Two notable neurodevelopmental genomic disorders: Potocki\u2013Lupski Syndrome (PTLS; MIM: 610883) and Smith\u2013Magenis Syndrome (SMS; MIM: 182290) are driven by LCRs that undergo NAHR between the directly oriented repeats causing a duplication (PTLS) or deletion (SMS) encompassing the dosage\u2010sensitive gene\n                    <jats:italic>RAI1<\/jats:italic>\n                    . We observed that other uncommon gains of varying sizes and extent at the 17p11.2 locus, which do not include the\n                    <jats:italic>RAI1<\/jats:italic>\n                    gene, could be found in patients ascertained with a neurodevelopmental delay (NDD) phenotype. We ascertained 15 individuals from 11 families with copy number gains at the 17p11.2 locus not encompassing the driver gene\u2014\n                    <jats:italic>RAI1<\/jats:italic>\n                    ; such individuals manifested a broad spectrum of neurodevelopmental phenotypes. To validate our genomic findings, investigate DNA rearrangement mechanism(s), and refine our understanding at the breakpoint junctions, we performed a combination of high\u2010resolution array CGH (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u200915), short\u2010read whole\u2010genome sequencing (sr\u2010GS,\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u20094), long\u2010read GS (lr\u2010GS; ONT;\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u20094 and PacBio HiFi;\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u20094), and breakpoint junctional analysis on this subset. Phenotypes in each individual were systematically studied. The phenotypes noted in these 15 individuals from 11 families primarily included developmental delay, intellectual disability, and behavioral problems. The genomic variations found in these 11 families included simple copy number gains (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u20097), higher order amplifications (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u20092), and complex genomic rearrangements (\n                    <jats:italic>n<\/jats:italic>\n                    \u2009=\u20092) at the 17p11.2 locus, surrounding the\n                    <jats:italic>RAI1<\/jats:italic>\n                    gene and not encompassing it. Individuals from 4\/11 families carried inherited variants. Identification of such rearrangement gains at the 17p11.2 locus that do not include the driver gene\n                    <jats:italic>RAI1<\/jats:italic>\n                    and yet research subjects still exhibit neurodevelopmental phenotypes creates an opportunity to (i) dissect the gene(s) and genetic mechanisms that might contribute to phenotypic variability at the PTLS locus and (ii) uncover previously unrecognized genes or disease pathways and mechanisms.\n                  <\/jats:p>","DOI":"10.1002\/ajmg.a.70234","type":"journal-article","created":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T04:17:02Z","timestamp":1784261822000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Copy Number Gains at 17p11.2 Sparing\n                    <scp>\n                      <i>RAI1<\/i>\n                    <\/scp>\n                    : A Shared Phenotype Pattern"],"prefix":"10.1002","author":[{"given":"Christopher M.","family":"Grochowski","sequence":"first","affiliation":[{"name":"Department of Molecular and Human Genetics Baylor College of Medicine  Houston Texas USA"},{"name":"Human Genome Sequencing Center Baylor College of Medicine  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shruti","family":"Pande","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics Baylor College of Medicine  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Parneet","family":"Kaur","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics Baylor College of Medicine  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haowei","family":"Du","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics Baylor College of Medicine  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zain","family":"Dardas","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics Baylor College of Medicine  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen J.","family":"Coveler","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics Baylor College of Medicine  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chelsi","family":"Rose","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics Baylor College of Medicine  Houston Texas USA"},{"name":"Texas Children's Hospital  Houston Texas USA"},{"name":"Department of Pediatrics Baylor College of Medicine  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Josephine","family":"Wincent","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine and Surgery Karolinska Institutet  Stockholm Sweden"},{"name":"Department of Clinical Genetics and Genomics Karolinska University Hospital  Stockholm Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shalini N.","family":"Jhangiani","sequence":"additional","affiliation":[{"name":"Human Genome Sequencing Center Baylor College of Medicine  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sravya V.","family":"Bhamidipati","sequence":"additional","affiliation":[{"name":"Human Genome Sequencing Center Baylor College of Medicine  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lorraine","family":"Potocki","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics Baylor College of Medicine  Houston Texas USA"},{"name":"Texas Children's Hospital  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"P. J.","family":"Hastings","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics Baylor College of Medicine  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer E.","family":"Posey","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics Baylor College of Medicine  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Lindstrand","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine and Surgery Karolinska Institutet  Stockholm Sweden"},{"name":"Department of Clinical Genetics and Genomics Karolinska University Hospital  Stockholm Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudia M. B.","family":"Carvalho","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics Baylor College of Medicine  Houston Texas USA"},{"name":"Pacific Northwest Research Institute  Seattle Washington USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James R.","family":"Lupski","sequence":"additional","affiliation":[{"name":"Department of Molecular and Human Genetics Baylor College of Medicine  Houston Texas USA"},{"name":"Human Genome Sequencing Center Baylor College of Medicine  Houston Texas USA"},{"name":"Texas Children's Hospital  Houston Texas USA"},{"name":"Department of Pediatrics Baylor College of Medicine  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5788-0270","authenticated-orcid":false,"given":"Davut","family":"Pehlivan","sequence":"additional","affiliation":[{"name":"Texas Children's Hospital  Houston Texas USA"},{"name":"Division of Neurology and Developmental Neuroscience, Department of Pediatrics Baylor College of Medicine  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,7,16]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1038\/387049a0","article-title":"Role for N\u2010CoR and Histone Deacetylase in Sin3\u2010Mediated Transcriptional Repression","volume":"387","author":"Alland L.","year":"1997","journal-title":"Nature"},{"key":"e_1_2_10_3_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1086\/380648","article-title":"The Breakpoint Region of the Most Common Isochromosome, i(17q), in Human Neoplasia Is Characterized by a Complex Genomic Architecture With Large, Palindromic, Low\u2010Copy Repeats","volume":"74","author":"Barbouti A.","year":"2004","journal-title":"American Journal of Human Genetics"},{"key":"e_1_2_10_4_1","doi-asserted-by":"crossref","first-page":"1310","DOI":"10.1016\/j.cell.2019.01.045","article-title":"Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2","volume":"176","author":"Beck C. 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