Splice-Site mutations in PKU

Splice-Site mutations in the PAH gene
[ .0001 PHENYLKETONURIA PAH, IVS12DS, G-A, +1]
[NCBI dbSNP - Short Genetic Variations database]

The most prevalent allele identified in persons of European descent with the metabolic disease Phenylketonuria (PKU) is a single base mutation (GT-to-AT in the DNA sense strand) that corresponds to a change from 5'-GU to 5'-AU in the splice donor site of Intron 12, as shown above. This makes the site unrecognizable by the splicing enzymes. During intron removal, the A site in Intron 12 bypasses the altered site in the 5'

3' direction (here, right to left), attaches incorrectly to the 5'-GU site of Intron 11, and excises Exon 12 along with Introns 11 & 12. Analysis of cDNA clones confirms that individuals with this mutation have the expected 156bp deletion in the mRNA, corresponding precisely to the length of Exon 12. This leads to a truncated PAH protein that lacks 52 amino acids at the C-terminus. This result is an unstable protein with almost zero PAH activity.

Note on terminology: exon and intron properly refer to regions of the DNA, which when transcribed as RNA, are respectively expressed and intervening. Corresponding regions in the RNA should properly be referred to as exon & intron equivalents. Even textbook authors slip up. The important point in this example is that the altered PAH protein results from a single-base pair mutation in the DNA, rather than deletion of Exon 12 as a length mutation in the genome.