Question

Any two human beings typically have an estimated 0.1% difference in their nucleotide sequences, which is equivalent to about 3 million nucleotide differences. These differences are the basis of the SNPs used to construct genetic linkage maps and are the basis for genotyping at 23andMe and Ancestry.com. Some of these SNPs actually lie in the region of the DNA that codes for protein, yet they have no effect on the phenotype of individuals carrying the SNP on both homologous chromosomes.

Provide three plausible explanations for how some SNPs can lie within the portion of the DNA that codes for the protein and yet have no discernible effect on the protein’s activity.

Answer 1

The reason why SNPs in protein coding regions may not affect protein activity are:

1. The substitution may be a silent mutation: Mutations that change the third base of a codon often do not change the Amino acid specified by the codon. This is known as a silent mutation.
2. The substitution may be an isofunctional mutation: Isofunctional mutations are mutations that substitute an Amino acid for another Amino acid with very similar properties. An example is a mutstion that substitutes a Aspartic Acid residue to a Glutamic Acid residue. Since both Amino Acids have similar properties the substitution of one for the other will not impact protein function.
3. The SNP may be in a non-coding region of the gene: Eukaryotic genes have several segments that are part of th coding region of the genome but do not code for protein directly but are rather involves in maintaining RNA stability. These regions include the 5' and 3' UTRs, and the Introns present in Eukaryotic genes.