Pathogenic variants in VPS53 are associated with pontocerebellar hypoplasia type 2E (PCH2E), characterized by microcephaly, severe neurodevelopmental impairment and epilepsy. We present a case of a female neonate with VPS53 pathogenic variants exhibiting the classic phenotypic features along with liver disease and deafness, which had not been described in previously reported cases. Similarly, while liver abnormalities have been reported in patients with mutations in other genes coding for proteins of the GARP or EARP complex, of which VPS53 is a subunit, liver disease has not been described in PCH2E until now. This case suggests that liver involvement may be an under-recognized feature of PCH2E and, more broadly, in GARP or EARP dysfunction, warranting further investigation.