Finding a rare causal mutation via WES is challenging, because variants changing protein-coding sequences are common (33); identifying sufficient recurrent mutations to confirm the candidacy of a specific gene requires resequencing of thousands of individuals (34) and parents if the goal is to define causal or contributory de novo mutations. Success varies by disorder. In ASD, WES in nearly 5000 probands across two large studies has demonstrated the contribution of rare de novo protein-disrupting mutations to disease risk, identifying 33 genes that are recurrently mutated and therefore highly likely to be pathogenic (4, 35). An additional several hundred mutant genes are observed only once in probands, each with an estimated 40% chance of being contributory, based on the frequency of similar events in controls (4). Overall, current estimates from families containing a single affected individual suggest that up to about 30% of cases harbor large-effect de novo coding mutations, due to either single-nucleotide variants or structural variants (4), each of which is rare in the population. As is the case with CNV (26, 36), inherited rare single-nucleotide variants also play a role in ASD (37), although their contribution warrants further refinement.
