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Bicuspid aortic valve and other left\u2010sided congenital heart lesions (LSL), including thoracic aortic aneurysms and acute aortic dissections, are 30\u201350 times more frequent in TS than in the general population. In 454 TS subjects, we found that LSL are significantly associated with reduced dosage of Xp genes and increased dosage of Xq genes. We also showed that genome\u2010wide copy number variation is increased in TS and identify a common copy number variant (CNV) in chromosome 12p13.31 that is associated with LSL with an odds ratio of 3.7. This CNV contains three protein\u2010coding genes (<jats:italic>SLC2A3<\/jats:italic>, <jats:italic>SLC2A14<\/jats:italic>, and <jats:italic>NANOGP1<\/jats:italic>) and was previously implicated in congenital heart defects in the 22q11 deletion syndrome. In addition, we identified a subset of rare and recurrent CNVs that are also enriched in non\u2010syndromic BAV cases. 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