A method of providing a diagnosis for a subject having Cowden-like syndrome or PTEN germline mutations is described. The method includes the steps of: (a) obtaining a biological sample from a subject; (b) conducting a germline PTEN mutation and deletion analysis of genomic DNA from the biological sample; (c) determining the level of copy number variation in the genomic DNA; (d) comparing the level of copy number variation in the genomic DNA to a control value for copy number variation; and (e) diagnosing the subject as having an increased risk of developing a neurodevelopmental disorder if the copy number variation level is higher than the control value.
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