The pathogenic homozygous variant in CHMP3 (chr2:g.8673460 G>A; NM_016079.4: c.518C>T; p.(Thr173Ile) was detected via Exome sequencing, in five patients. Functional assays revealed reduced expression of the CHMP3 protein in patient’s cells, which perturbed autophagy process, causing accumulation of endosomes and autophagosomes, within patients cell lines.