Abstract: It was discovered that, for individuals with certain types of mutations, clinical outcomes or phenotypes can be very accurately predicted. For example, for an individual with autism harboring a de novo LGD mutation, the patient’s IQ, behavioral phenotypes, and motor/movement phenotypes, and the severity of autism can be predicted. For these LGD mutations, due to a mRNA surveillance mechanism called NMD (nonsense-mediated decay), it was discovered that clinical outcomes and phenotypes are strongly correlated with the expression intensity of the exon harboring the mutation. A method/model was developed, which is called PDS (phenotype dosage sensitivity), to predict phenotypes based on this observation, and the model is able to predict phenotypes at a much higher level of accuracy not previously possible. This disclosure is the first to link LGD mutations and clinical phenotypes in this manner.