Next-generation sequencing has become a valuable tool for detecting mutations involved in Mendelian diseases. However, it is a challenge to identify the small subset of functionally important mutations from tens of thousands of rare variants in a whole exome/genome. Therefore, we developed a toolkit called PriVar, a systematic prioritization pipeline that takes into consideration calling quality of the variants, their predicted functional impact, known connection of the gene to the disease and the number of mutations in a gene, and inference from linkage analysis.