Many neurodevelopmental disorders are caused by the presence of CNVs. Chromosome microarray technology is widely used to accurately detect CNVs. We report the case of a male, aged 3 years, presenting with delayed psychomotor development, generalized hypotonia, encephalopathy, delayed myelination in the central nervous system, and poor motor coordination. The array CGH revealed an interstitial deletion of chromosome 19q13.2 with a size of 88.8 kb involving 3 OMIM genes: <i>RABAC1</i>, <i>ARHGEF1</i>, and <i>ATP1A3</i>. Heterozygous mutations in the <i>ATP1A3</i> gene are associated with delayed psychomotor development, alternating hemiplegia of childhood type 2 (AHC2), dystonia type 12, and cerebellarataxia-areflexia–pes cavus-optic atrophy-sensorineural hearing loss syndrome, also called CAPOS syndrome. The phenotypic expression of partial <i>ATP1A3</i> deletion is, however, poorly described in the literature. The deletion was confirmed by MLPA, and we identified a hitherto undescribed novel deletion of exons 3b–21 of the <i>ATP1A3</i> gene. Our data suggest that the deletion of the <i>ATP1A3</i> gene is a causative factor of the AHC2 phenotype in the patient.