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To explain: Why most of the nucleotide variability within a genetic locus does not affect the phenotype.
Introduction: Variation at a genetic locus can be defined as any change in the nucleotide sequence of the DNA caused due to mutations occurred in that locus of the gene. However, most of the nucleotide variability does not affect the phenotype because mutations that occur in the non-coding region do not alter/change the amino acid sequence, which codes for the proteins
Explanation of Solution
Higher organisms have a large gene pool that contains non-coded DNA known as introns. As most of the nucleotide variability due to mutations occurs in the intron region, it does not cause a change in amino acid and do not code for a protein, which leads to the neutral effect in the population. Only the nucleotide variations in the coding region have a significant impact if the change in DNA sequence leads to a change in the amino acid sequence to alter the proteins structure and function. Although most variable regions within exons reflect changes in the DNA sequence and most of them do not change the sequence of amino acids encoded by a gene, they do not affect the phenotype.
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