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Every gene mutation may not alter the protein that is coded by the gene. There are several reasons for this.
A gene is a part of the entire DNA, which gets transcribed into an mRNA and then gets translated into a protein.
When a gene gets mutated, the type of mutation has a great effect on the result that it produces. It may be the big, chromosomal mutation to the point mutation at a single base. Whatever type of mutation it is, it has an effect on the organism when the product coded by the gene is altered. There are chances that the mutated base sequence codes for the same protein as the non-mutated one, which is a blessing of the degeneracy of the genetic code. There are 64 different combinations of the bases which ultimately codes for only 21 amino acids. ie., more than one codon for a single amino acid. This helps in nullifying many mutations.
The entire bases seen in a gene are all not seen in the mRNA transcribed from it. Many are removed in the several processing steps that form the mRNA which is ready for translation. If the mutation occured in those deleted regions, it not going to alter the protein.
Again, all part of the mRNA is not going to be seen in the final active folded protein. Post-translational process removes several regions. So this again lessens the probability of the mutation to take effect.
Thus every gene mutation may not cause an alteration in the final protein that it codes.
Here is the best answer I could find for your question and I have quoted the entire answer because it was answered very well and I think it makes the most sense:
Not every gene mutation causes alteration in the composition of the protein the gene codifies. Since the genetic code is degenerated, i.e., there are amino acids codified by more than one different DNA nucleotide triplet, if by chance the mutation substitutes one or more nucleotides of a codifier triplet and the newly formed triplet still codifies the same amino acid codified by the original triplet there will be no modification in the protein made from the gene. (Karyotype and genetic diseases, link listed below)
I also listed the enotes.com link for mutations which contains a lot of very useful information.
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