Yunis-Varón syndrome caused by biallelic VAC14 mutations

Matthew A Lines, Yoko Ito, Kristin D Kernohan, Wendy Mears, Julie Hurteau-Miller, Sunita Venkateswaran, Leanne Ward, Karine Khatchadourian, Jeff McClintock, Priya Bhola, Philippe M Campeau, Kym M Boycott, Jean Michaud, André BP van Kuilenburg, Sacha Ferdinandusse, David A Dyment

Yunis-Varón syndrome (YVS) is an autosomal recessive disorder comprising skeletal anomalies, dysmorphism, global developmental delay and intracytoplasmic vacuolation in brain and other tissues. All hitherto-reported pathogenic variants affect FIG4, a lipid phosphatase involved in phosphatidylinositol (3,5)-bisphosphate [PtdIns(3,5)P2] metabolism. FIG4 interacts with PIKfyve, a lipid kinase, via the adapter protein VAC14; all subunits of the resulting complex are essential for PtdIns(3,5)P2 synthesis in the endolysosomal membrane compartment. Here, we present the case of a female neonate with clinical features of YVS and normal FIG4 sequencing; exome sequencing identified biallelic rare coding variants in VAC14. Cultured patient fibroblasts exhibited a YVS-like vacuolation phenotype ameliorated in a dose-dependent fashion by ML-SA1, a pharmacological activator of the lysosomal PtdIns(3,5)P2 effector TRPML1. The patient developed a diffuse leukoencephalopathy with loss of the normal N-acetylaspartate spectrographic peak and presence of a large abnormal peak consistent with myoinositol. We report that VAC14 is a second gene for Yunis-Varón syndrome.European Journal of Human Genetics advance online publication, 21 June 2017; doi:10.1038/ejhg.2017.99.