Schematic representation of the microdeletions on 7q21.3 associated with SHFM. In three families (Family 1, 3 and 4) with an autosomal dominant non-syndromic SHFM phenotype overlapping microdeletions were detected. The deletions encompass the eExons 15 and 17 of DYNC1I1 (red) as well as the last three exons of SLC25A13 including the enhancer elements eDlx#23 (blue) within its intronic region driving expression in otic vesicle. The DYNC1I1 exons 15 and 17 have previously been shown to act as tissue-specific enhancers of Dlx5/6 in mouse and zebrafish . In family 2 presenting with SHFM and hearing loss a 510 kb deletion was identified including the eExons of DYNC1I1 but also SLC25A13, C7orf76, the brain enhancer element hs1642 and two branchial arch enhancers (green) . The deletion of hs1642 might be responsible for hearing loss in family 2. The SHFM family reported by Kouwenhoven et al. developed hearing loss during adolescents . P1- P4 indicated the qPCR amplicons used in this study. Breakpoint sequences are shown in Additional file 1: Figure S1.