Neutral (or silent or synonymous) mutations occur when the change of a single DNA nucleotide (A,T,C,G) within a gene does not affect the sequence of amino acids that make up the gene’s protein (15). The sequence of amino acids determines the 3-D structure of the protein, and that determines the function of the protein in the cell, and that determines the fitness of the organism. So, if the protein is not changed it will have no effect on the phenotype and the fitness of the organism. In other words: it will be neutral.
My thoughts: There are no neutral mutations. A mutation that creates a synonomous codon will still effect transcription frequency, either increasing frequency or decreasing frequency. The tRNA, responsible for retrieving a specific base, may be under or overexpressed for the mutated codon. Even though the codon codes for the same amino acid the speed at which a protein is translated will be effected. This could have many downstream effects.