In what ways can a point mutation affect the protein encoded for by a gene?

Point mutations can affect a protein in various ways, depending on the type of point mutation that has occurred. Substitution mutations can be silent, causing no change in the end protein; they can cause missense mutations, where a single amino acid is switched for another; or they can be nonsense mutations, where a stop codon replaces one coding for an amino acid. The effect of a missense mutation varies depending on the swap that has occurred, ranging from completely de-functioning the protein to making relatively small alterations in its shape and action. Nonsense mutations are more severe the earlier in a gene they happen, as they prematurely terminate the synthesis of the protein at the affected codon.

Insertion and deletion mutations cause frameshift mutations and are also increasingly severe the earlier they occur, as they add or remove a nucleotide to the genetic sequence – disrupting the parsing of codons from the point at which they occur onwards. The resulting protein has the normal order of amino acids until the point of the mutation, beyond which the sequence is virtually unrecognizable when compared to the original. This almost always has significant implications for the end structure of the protein, rendering it essentially useless.

Also note - splice site mutations can also occur, causing parts of exons to be omitted or parts of introns included in the final protein product. These are more complicated to understand and should be the topic of another lesson/question.