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Background  Rubinstein-Taybi syndrome (RSTS; OMIM #180849, #613684) is a rare autosomal dominant genetic condition characterized by broad thumbs and halluces, facial dysmorphism, short stature and variable degree of intellectual disability. RSTS is associated with mutations in  CREBBP  and  EP300  genes in 50–60% and 5–8% of cases, respectively. The majority of cases are  de novo  heterozygous mutations.    Case presentation  Here we describe a familial RSTS case, associated with a novel  EP300  mutation. The proband was a 9 years old female, with mild learning difficulties. Her mother, who also had learning difficulties, was found to have short and broad thumbs. MLPA and panel-based NGS of  CREBBP  and  EP300  were performed. A novel heterozygous frameshift mutation in exon 31 of the  EP300  gene (c.7222_7223del; p.(Gln2408Glufs*39)) was found in both.    Conclusions  This case represents the first case of inherited  EP300 -RSTS. The location of the frameshift deletion not affecting HAT domain and PHD finger, could explain the mild phenotype and the well-preserved intelligence. These patients are mildly affected, and this case highlights the possible missed diagnosis. We would recommend molecular testing of apparently healthy parents, and in the case of inherited mutations, of all adult first degree relatives at risk.    Electronic supplementary material  The online version of this article (doi:10.1186/s12881-016-0361-8) contains supplementary material, which is available to authorized users.

First case report of inherited Rubinstein-Taybi syndrome associated with a novel EP300 variant