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The male Y\u2010chromosome aneuploidy XYY is associated with physical, behavioral\/cognitive phenotypes, and autism spectrum disorders. We hypothesize that increased risk for these phenotypes is caused by increased copy number\/overexpression of Y\u2010encoded genes. Specifically, an extra copy of the neuroligin gene <jats:italic>NLGN4Y<\/jats:italic> might elevate the risk of autism in boys with XYY. We present a unique male with the karyotype 46,X,idic(Y)(q11.22), which includes duplication of the Y short arm and proximal long arm and deletion of the distal long arm, evaluated his physical, behavioral\/cognitive, and neuroimaging\/magnetoencephalography (MEG) phenotypes, and measured blood RNA expression of Y genes. The proband had tall stature and cognitive function within the typical range, without autism features. His blood RNA showed twofold increase in expression of Yp genes versus XY controls, and absent expression of deleted Yq genes, including <jats:italic>NLGN4Y<\/jats:italic>. The M100 latencies were similar to findings in typically developing males. In summary, the proband had overexpression of a subset of Yp genes, absent <jats:italic>NLGN4Y<\/jats:italic> expression, without ASD findings or XYY\u2010MEG latency findings. These results are consistent with a role for <jats:italic>NLGN4Y<\/jats:italic> overexpression in the etiology of behavioral phenotypes associated with XYY. Further investigation of <jats:italic>NLGN4Y<\/jats:italic> as an ASD risk gene in XYY is warranted. The genotype and phenotype(s) of this subject may also provide insight into how Y chromosome genes contribute to normal male development and the male predominance in ASD.<\/jats:p>","DOI":"10.1002\/ajmg.b.32745","type":"journal-article","created":{"date-parts":[[2019,6,4]],"date-time":"2019-06-04T08:14:50Z","timestamp":1559636090000},"page":"471-482","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Y chromosome gene copy number and lack of autism phenotype in a male with an isodicentric Y chromosome and absent NLGN4Y expression"],"prefix":"10.1002","volume":"180","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5991-964X","authenticated-orcid":false,"given":"Judith L.","family":"Ross","sequence":"first","affiliation":[{"name":"Department of Pediatrics Nemours DuPont Hospital for Children, Thomas Jefferson University  Philadelphia Pennsylvania"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luke","family":"Bloy","sequence":"additional","affiliation":[{"name":"Lurie Family Foundations MEG Imaging Center, Department of Radiology Children's Hospital of Philadelphia  Philadelphia Pennsylvania"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Timothy P. 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