In the past few years the number of copy number variants (CNVs) identified in the human genome has increased significantly, but our understanding of the functional impact of CNVs is still limited. Clinically significant variations cannot easily be distinguished from benign, complicating interpretation of patient data. Multiple studies have focused on analysis of regions that vary in copy number in specific disorders. Here we use the opposite strategy and focus our analysis on regions that never seem to vary in the general population, hypothesizing that these are copy number stable because variations within them are deleterious. Our results show that copy number stable regions are characterized by correlation with a number of genomic features, allowing us to define a list of genomic regions that are dosage sensitive in humans. We find that these dosage-sensitive regions show significant overlap with de novo CNVs identified in patients with intellectual disability or autism. There is also a significant association between copy number stable regions and rare inherited variants in autism patients, but not in controls. Based on this predictive power, we propose that copy number stable regions can be used to complement maps of known CNVs to facilitate interpretation of patient data.