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Background  Tight control of endosome trafficking is essential for the generation of a normally patterned embryo. Recent studies have found that VPS50 is a key ingredient in EARP which is required for recycling of internalized TfRs to the cell surface and dense-core vesicle maturation. However, the role of  VPS50  in embryogenesis and human physiology are poorly understood.    Results  We identified a rare missense heterozygous  VPS50  mutation (p. Gly169Val) in NTDs by high-throughput sequencing. In vitro functional analysis demonstrated that the p. Gly169Val was a loss-of-function mutation, delaying transferrin recycling and altering its interaction with VPS53. Using WISH during zebrafish embryogenesis, we demonstrated that  vps50  gene was expressed throughout the early embryo, especially in the head. Abnormal body axis phenotypes were observed in those  vps50  knock-down zebrafishes. Further rescue study in zebrafish suggested that the mutation displayed loss-of-function effects comparing with wild-type  VPS50 .    Conclusions  These findings thus demonstrated that the functional mutations in  VPS50  might contribute to neurodevelopmental disorder and highlighted the critical importance of  VPS50  function in cellular and organismal physiology.    Electronic supplementary material  The online version of this article (10.1186/s13039-019-0421-9) contains supplementary material, which is available to authorized users.

The rare mutation in the endosome-associated recycling protein gene VPS50 is associated with human neural tube defects