Translocations within the TFE gene resulting in oncogenic fusion proteins have been associated with multiple neoplasms. De novo mutations in the X-linked gene TFE3 in exons 3 and 4 are considered to contribute to lysosomal storage disorder-like features. However, the histologic findings within the livers of patients with TFE3 mutations are not well characterized. The authors report a case of a 12 day old term male who was admitted to the pediatric intensive care unit and went on to develop worsening direct hyperbilirubinemia and hepatomegaly. Due to the constellation of clinical findings, whole genome sequencing was performed and a rare de novo hemizygous mutation was identified in the TFE3 gene (c.560C >
T
p.Thr187Met) which was thought to be likely pathogenic. The patient subsequently had 2 liver biopsies performed, both with similar histologic findings. The liver was found to have a giant cell hepatitis pattern of injury with severe cholestasis and extensive pseudorosette formation. Additional studies are needed to understand the histologic changes which could be associated with mutations in the TFE3 gene. The impact of a TFE3 mutation on the liver represents an area where further study is necessary to provide prognostic and therapeutic guidance for future patients.