I annotated some variations (SNP) using VEP, there are two stop gain mutations, one at 2nd amino acid and another at the 110th amino acid position (the protein has about 300 amino acid). While the VEP says their impact is "HIGH", but it didn't return any value for SIFT or polyphen, could you please let me know why? Given the position of stop gain mutation, can we say the related protein is certainly truncated and non-functional at least at the bioinformatic analysis level?
As the last question, sorry, could you please suggest any database/server to check the conserved amino acids (not domain) within the protein?
Many thanks in advance