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Germline pathogenic variants in  RUNX1  are associated with familial platelet disorder with predisposition to myeloid malignancies (FPD/MM) with intragenic deletions in  RUNX1  accounting for almost 7% of all reported variants. We present two new pedigrees with FPD/MM carrying two different germline  RUNX1  intragenic deletions. The aforementioned deletions encompass exons 1–2 and 9–10 respectively, with the exon 9–10 deletion being previously unreported. RNA sequencing of patients carrying the exon 9–10 deletion revealed a fusion with  LINC00160  resulting in a change in the 3′ sequence of  RUNX1 . Expression analysis of the transcript isoform demonstrated altered  RUNX1a/b/c  ratios in carriers from both families compared to controls. Our data provide evidence on the impact of intragenic  RUNX1  deletions on transcript isoform expression and highlight the importance of routinely performing copy number variant analysis in patients with suspected MM with germline predisposition.

leukemia and lymphoma

Familial platelet disorder due to germline exonic deletions in  RUNX1 : a diagnostic challenge with distinct alterations of the transcript isoform equilibrium