Consequences of DNA mutations depend on their position in the gene region

    For this hyhypothetical gene, the complete gene includes protein-coding exons, as well as intervening introns, and flanking control regions such as upstream (5') promoters and enhancers in upstream & downstream (3') regions.

m1: Mutations in the promoter region may affect gene transcription
may lead to non-functional (null) alleles.
m2: Mutations in exons, if they result in the substitution of an amino acid in the active site or other critical region of the protein, also lead to alleles with modified (reduced) functionality.
m3: In contrast, exon mutations that result in changes outside the active sites or at 3rd codon positions may have little or no effect on gene function.
             These mutations are called silent (if the amino acid is unchanged) or neutral (if the change has no effect).
m4: Mutations at critical positions near intron / exon junctions may affect mRNA splicing and lead to the deletion or retention of entire exons, and result in null alleles.
m5: Mutations that occur
in non-coding introns, or
5' or 3' flanking portions of the gene, may have little or no effect on gene function.

Figure modified from Klug & Cummings 1997; All text material © 2014 by Steven M. Carr