CtIPDelta
The deletion is in fact 1653 nucleotides (I had missed a micro-homology event at the break site in the original description). The break points, relative to the CtiP gene sequence (1 = start of 5' UTR) are nucleotides 137-1789. This corresponds to amino acids 2 through 465 (out of 493) of the CtiP isoform A, with the last 29 amino acids out of reading frame. 
In terms of amino acid sequence, the deletion starts at the second nucleotide of amino acid 2, and ends just before the first nucleotide of amino acid 466.