After recognising that limited clinical information on the parental phenotype (or incomplete penetrance, or both) might lead to removal of pathogenic inherited developmental disorder gene variants from the dataset (as exemplified by Noonan syndrome variants in RIT1 and PTPN11), we recommend that the bioinformatics pipeline includes strategies to address this issue, such as a whitelist of annotated pathogenic variants and predicted pathogenic (truncating) variants in developmental disorder genes that are not removed from the dataset, even if inherited from an apparently unaffected parent. The gene discussed is PTPN11; the disease is Noonan syndrome.