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Background  Achondroplasia is a well-defined and common bone dysplasia. Genotype- and phenotype-level correlations have been found between the clinical symptoms of achondroplasia and achondroplasia-specific   FGFR3  mutations.    Result  A 2-year-old boy with clinical features consistent with achondroplasia and Silver-Russell syndrome-like symptoms was found to carry a mutation in the fibroblast growth factor receptor-3 (FGFR3) gene at c.1138G > A (p.Gly380Arg) and a  de novo  574 kb duplication at chromosome 7p12.1 that involved the entire growth-factor receptor bound protein 10 (GRB10) gene. Using quantitative real-time PCR analysis,  GRB10  was over-expressed, and, using enzyme-linked immunosorbent assays for  IGF1  and IGF-binding protein-3 (IGFBP3), we found that  IGF1  and  IGFBP3  were low-expressed in this patient.    Conclusions  We demonstrate that a combination of uncommon, rare and exceptional molecular defects related to the molecular bases of particular birth defects can be analyzed and diagnosed to potentially explain the observed variability in the combination of molecular defects.    Electronic supplementary material  The online version of this article (doi:10.1186/s13023-016-0465-4) contains supplementary material, which is available to authorized users.

FGFR3 gene mutation plus GRB10 gene duplication in a patient with achondroplasia plus growth delay with prenatal onset