An intragenic deletion in the human PTPN6 gene is described. The PTPN6
gene maps to chromosome 12p12-13 and is shown to possess two alternat
ive first exons. A 1.7-kb deletion occurring in the intron between the
two alternatively used first exons is the result of an illegitimate r
ecombination between two Alu-type repeats. The deletion increases the
transcriptional activity of the distal promotor.