RNAMute is an interactive web tool written in Java that calculates the secondary structure of all single point mutations, given an RNA sequence, and organizes them into categories according to their distances from the wildtype predicted structure. The secondary structure predictions are performed using the Vienna RNA package. Several alternatives are used for the categorization of single point mutations: Vienna?s RNADistance based on dot-bracket representation, tree edit distance, and second eigenvalue of the Laplacian matrix based on Shapiro?s coarse grain treegraph representation. Selecting a category in each one of the tables lists all single point mutations belonging to that category. Selecting a mutation displays a graphical picture of the single point mutation and the wildtype, and includes basic information such as associated energies, representations, distances. RNAMute is a user friendly tool that can be used to predict single point mutations leading to conformational rearrangements in the secondary structure of RNAs.