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Background  Achromatopsia (ACHM) is a severe congenital autosomal recessive retinal disorder caused by loss of cone photoreceptors. Here, we aimed to determine the underlying genetic lesions and phenotypic correlations in two Chinese families with ACHM.    Methods  Medical history and clinical evaluation were obtained from both families. Targeted exome sequencing (TES) was performed on 201 disease-causing genes of inherited retinal dystrophies to screen for ACHM causative mutations in the two probands.    Results  The compound heterozygous mutations in  CNGA3  (c.1074G > A, p.W358X; c.1706G > A, p.R569H) were identified in the first proband, and a novel homozygous mutation (c.968C > A, p.A323D) was detected in the other pedigree. The proposed topological model of the  CNGA3  polypeptide suggested that the missense mutations primarily affected the transmembrane helix 5 and the cGMP-binding domain, respectively. Crystal structure modeling of the cyclic nucleotide-gated cation channel α-3 (CNGA3) protein encoded by the  CNGA3  gene revealed an abnormal combined structure generated by R569H.    Conclusions  We firstly used the TES approach to identify genetic alterations in patients with ACHM. We uncovered three mutations in  CNGA3 , including one novel mutation. Our results not only expand the genotypic spectrum for  CNGA3  mutations, but also demonstrate that the TES approach is a valuable tool for molecular diagnosis.    Electronic supplementary material  The online version of this article (doi:10.1186/s12967-015-0694-7) contains supplementary material, which is available to authorized users.

Identification of novel mutations by targeted exome sequencing and the genotype-phenotype assessment of patients with achromatopsia