By using an integrated omics approach, we investigated the functional consequences of a de novo intragenic deletion of GTDC1 (MIM *610165), encoding a putative glycosyltransferase, which was detected through routine CMA testing in a female individual with developmental encephalopathy including ID, epilepsy, microcephaly, speech delay, and facial dysmorphisms. This evidence concerns the gene QTMAN and epilepsy.