I am currently a IT student and try to become a bioinformatician, and that is, I have a little knowledge of molecular biology. Now, perhaps my question is so dumb, but It took several days and I still coundnt see the solution. To my understanding, nonsynonymous mutation is a mutation that alters the amino acid sequence of a protein. Now, I have mutation groups including: missense, silent, splice-site, nonsense, splice-region, TSS, nonstop mutation and indel, and I think that, missense, nonsense and indel are three kinds of non-synonymous mutation. Is It correct or not? Please correct me if I am wrong. Thank in advance.
"Non-synonymous" is typically used as a synonym for "missense", it's used specifically to describe the situation where a codon changes so that it encodes a different amino acid. This is in contrast to a "synonymous" variant where the codon changes but it still encodes the same amino acid.
"Nonsense" is where it changes to a stop codon. Even though this changes the amino acid sequence, it is considered separately to missense/non-synonymous variants because it is more severe.
"Indel" is a classification of a type of variant, rather than a consequence of the variant. An "indel" just means that some bases are inserted or deleted. It may or may not fall within a protein coding region, which means it may or may not affect the amino acid sequence. Within a protein coding sequence it may be an "in-frame insertion/deletion", which means that the number of bases inserted/deleted is a multiple of three, meaning that amino acids are simply inserted/deleted, and only those amino acids are affected. Or it can be a "frameshift insertion/deletion", which means that it's not a multiple of three, and will mess up all the codons downstream of it. Frameshifts are usually more severe than in-frame, which are in turn more severe than indels outside of a protein.
"Nonsynonymous" is quite out-of-date terminology and is not the standard phrasing used by Sequence Ontology.
