NRXN1 microdeletions occur at relatively high frequency and confer increased risk for neurodevelopmental and neurobehavioral abnormalities.The mechanism that makes NRXN1 a deletion hotspot is unknown.Here, we identified deletions of the NRXNlregion in case cohorts,confirming a strong association with autism spectrum and other neurodevelopmental disorders.Interestingly, deletions in both cases and controls were clustered in the 5portionofNRXN1 and its immediate upstream region.To explore the mechanism of deletion, we mapped and analyzed the breakpoints of 32 deletions.