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Background  Copy number variations play a significant role in the aetiology of developmental disabilities including non-syndromic intellectual disability and autism.    Case presentation  We describe a 19-year old patient with intellectual disability and autism for whom chromosomal microarray (CMA) analysis showed the unusual finding of two  de novo  microdeletions in cis position on chromosome 6q16.1q16.2 and 6q16.3. The two deletions span 10 genes, including  FBXL4, POU3F2, PRDM13, CCNC, COQ3  and  GRIK2 . We compared phenotypes of patients with similar deletions and looked at the involvement of the genes in neuronal networks in order to determine the pathogenicity of our patient’s deletions.    Conclusions  We suggest that both deletions on 6q are causing his disease phenotype since they harbour several genes which are implicated in pathways of neuronal development and function. Further studies regarding the interaction between  PRDM13  and  GRIK2  specifically may be interesting.

Autism and intellectual disability in a patient with two microdeletions in 6q16: a contiguous gene deletion syndrome?