Updated project metadata. First described in Drosophila melanogaster, planar cell polarity (PCP) is a developmental process essential for embryogenesis and development of polarized structures in Metazoans. This signaling pathway involves a set of evolutionarily conserved genes encoding transmembrane (Vangl, Frizzled, Celsr) and cytoplasmic (Prickle, Dishevelled) molecules. Vangl2 is of major importance in embryonic development as illustrated by its pivotal role during neural tube closure in human, mouse, Xenopus and zebrafish embryos. The regulated and poorly understood traffic of Vangl2 to the plasma membrane is a key event for its function in development. Here we identify a novel N-terminally extended isoform of Vangl2, termed Vangl2-Long that arises from the use of non-AUG start codon upstream of the coding region of canonical Vangl2. Vangl2-Long contains an evolutionarily conserved N-terminal 48 amino acid sequence bearing a signal for subcellular localization in the Golgi apparatus. Moreover, we provide data in Xenopus showing that Vangl2-Long is important for correct convergent extension movements and neural tube closure. These data describe a further level of complexity in Vangl2 expression, trafficking and function.