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Amongst silent, nonsense and missense genetic mutations, is the latter the only one that leads to the creation of new alleles?

If we define alleles as a specific form of a gene, and a gene as a heritable factor consisting of a length of DNA that influences a certain characteristic, since the missense mutation is the only one that leads to the physical creation of a new protein, is it not the only one that would lead to the creation of new alleles?

Or would nonsense also lead to new alleles as the lack of the protein may lead to the expression of a different characteristic?

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  • $\begingroup$ Its a good question actually as allele concept confuses a lot of people. I am sure it will be helpful for lot of people in future Insha'Allah $\endgroup$
    – Failed Scientist
    May 2 '16 at 0:49
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So the term allele is a broad one, and simply refers to the different versions of any piece of DNA in circulation in the gene pool - it doesn't need to refer to a gene. I can talk about the alleles at a random place in the genome.

But if we proceed with your question and ask - 'do nonsense mutations within coding genes also lead to the creation of different proteins' - the answer is 'sometimes'. A nonsense mutation is just one that introduces a stop codon. The result is an mRNA that codes for a shortened protein. Sometimes, the mRNA will be recognized as faulty and degraded, and so little to no protein gets made. Sometimes, if made, that protein will be unstable, or the result will be as if no protein had been made. Sometimes though, the protein will be stable, and could hang around uselessly, or even do damage.

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    $\begingroup$ Allele is indeed a very broad term. Easily the term which confused me the most in the whole Molecular Biology. And +1 for the last part. I liked the explanation. $\endgroup$
    – Failed Scientist
    May 1 '16 at 15:08
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    $\begingroup$ And sometimes the truncated protein can be useful for a different function. For example, apolipoprotein-B. $\endgroup$
    – WYSIWYG
    May 2 '16 at 5:33
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Allele is just a variant form of gene: independent of the final product of protein, so nonsense will also lead to new allele. I will quote Nature Scitable here:

Alleles can also refer to minor DNA sequence variations between alleles that do not necessarily influence the gene's phenotype.

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