An individual genotype is composed of two distinct parts, the inherited sequences from the maternal and paternal genomes. Therefore, for every genotype, there are two copies of the sequence. For genes, we refer to these individual sequence copies on each chromosome that make up a genotype as the two alleles. Alleles may be identical or different, and various combinations of alleles can create a range of phenotypes.
A DNA change within a gene may or may not alter the protein that is encoded by the gene. If the change contributes to normal genetic variability and is found in more than 1 percent of the population being studied, the variation is called a polymorphism. Variations in a gene that modify, seriously disrupt, or prevent the functioning the encoded protein are called mutations. The effect of a mutation can range from harmless to harmful depending on the type of mutation.
One type of sequence variation is the substitution of one nucleotide for another, which can thus affect the three base-pair unit (codon) that codes for a specific amino acid. In some cases, where the substitution does not change the amino acid, the result is a neutral or silent mutation. A substitution that alters the coding sequence, and thus substitutes a different amino acid, is called a missense mutation. This type of mutation can have a beneficial effect whereby there is a positive gain of function for the protein, it can also have a drastically negative effect and result in loss of function or the gain of a new function that is deleterious to the organism. By far the most severe change is a nucleotide substitution that creates a stop codon where one should not be. This phenomenon, called a nonsense mutation, will prevent the full formation of the protein. A nonsense mutation can completely abolish the function of the protein, which can be lethal to the organism if the protein is essential for sustaining a key biological process.
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