Pa2G4 binds to Six1 and interferes with the Six1-Eya1 complex. Pa2G4 knock-down reduces neural border, neural crest and cranial placode genes. Increasing Pa2G4 expands neural crest genes mostly at the expense of placode genes. Both alterations cause later defects in branchial arch and otocyst gene expression. We suggest pa2g4 as a candidate gene for Branchiootorenal Spectrum disorder.