Putative mechanism underlying the large atypical NF1 deletions identified in patient ASB4-55 and the grandmother of patient DA-77. The deletions were associated with the insertion of an SVA element mediated by the LINE 1 protein machinery via target-primed reverse transcription. (A) SUZ12P intron 8 is indicated in lilac whereas the telomeric part of the NF1 region is shown in green. The dotted lines indicate the approximately 1-Mb distance between these two regions. The SVA insertion within SUZ12P intron 8 is likely to have been initiated by the L1 endonuclease (L1-EN), which will have introduced a nick at the consensus cleavage site 5′-CTTT/A-3′. (B) Next, the SVA mRNA annealed to the T-overhang by means of its polyA-tail. Then, the L1 reverse transcriptase used the SVA mRNA as a template for reverse transcription to synthesize the SVA cDNA (blue). Second strand cleavage by the L1-EN occurred upstream of the first-strand cleavage site. Independently, a double strand break (DSB) occurred in the telomeric region of 17q11.2. (C,D) After dissociation of the SVA mRNA, the integration process was not finalized by recombinational repair using the downstream SUZ12P intron 8 sequence. Instead, the DNA ends were ligated by NHEJ to the open-ended DNA sequence located within the telomeric 17q11.2 region, between the RAB11FIP4 and COPRS genes, which resulted in the deletion of the intervening sequence and hence the occurrence of the atypical NF1 deletion (D).