In the proband RP-3055 suffering from a complex presentation of syndromic cone-rod dystrophy, we identified a heterozygous microdeletion of ~ 16.5 Mb on 3q11.2q13.31 (hg19: chr3:97483365-113953480), involving at least 60 OMIM genes, which included ARL6 (Bardet-Biedl syndrome, MIM #600151), IMPG2 (retinitis pigmentosa, MIM #613581; and macular dystrophy, vitelliform, MIM #616152), ZBTB11 (Intellectual developmental disorder, MIM #618383), and ATP6V1A (developmental and epileptic encephalopathy, MIM #618012), among others. Here, ATP6V1A is linked to Cone rod dystrophy.