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Background  We report on a young female, who presents with a severe speech and language disorder and a balanced  de novo  complex chromosomal rearrangement, likely to have resulted from a chromosome 7 pericentromeric inversion, followed by a chromosome 7 and 11 translocation.    Results  Using molecular cytogenetics, we mapped the four breakpoints to 7p21.1-15.3 (chromosome position: 20,954,043-21,001,537, hg19), 7q31 (chromosome position: 114,528,369-114,556,605, hg19), 7q21.3 (chromosome position: 93,884,065-93,933,453, hg19) and 11p12 (chromosome position: 38,601,145-38,621,572, hg19). These regions contain only non-coding transcripts (ENSG232790 on 7p21.1 and TCONS_00013886, TCONS_00013887, TCONS_00014353, TCONS_00013888 on 7q21) indicating that no coding sequences are directly disrupted. The breakpoint on 7q31 mapped 200 kb downstream of  FOXP2 , a well-known language gene. No splice site or non-synonymous coding variants were found in the  FOXP2  coding sequence. We were unable to detect any changes in the expression level of  FOXP2  in fibroblast cells derived from the proband, although this may be the result of the low expression level of  FOXP2  in these cells.    Conclusions  We conclude that the phenotype observed in this patient either arises from a subtle change in  FOXP2  regulation due to the disruption of a downstream element controlling its expression, or from the direct disruption of non-coding RNAs.    Electronic supplementary material  The online version of this article (doi:10.1186/s13039-015-0148-1) contains supplementary material, which is available to authorized users.

Language impairment in a case of a complex chromosomal rearrangement with a breakpoint downstream of FOXP2