A first clathrate compound with selenium guest atoms, [Ge46-xPx]Se8-y square(y) (x = 15.4(1); y = 0-2.65; square denotes a vacancy), was synthesized as a single-phase and structurally characterized. It crystallizes in the space group Fm (3) over bar with the unit cell parameter a varying from 20.310(2) to 20.406(2) angstrom and corresponding to a 2 x 2 x 2 supercell of a usual clathrate-I structure. The superstructure is formed due to the symmetrical arrangement of the three-bonded framework atoms appearing as a result of the framework transformation of the parent clathrate-I structure. Selenium guest atoms occupy two types of polyhedral cages inside the positively charged framework; all selenium atoms in the larger cages form a single covalent bond with the framework atoms, relating the title compounds to a scanty family of semiclathrates. According to the measurements of electrical resistivity and Seebeck coefficient, [Ge46-xPx]Se8-y square(y) is an n-type semiconductor with E-g = 0.41 eV for x = 15.4(1) and y = 0; it demonstrates the maximal thermoelectric power factor of 2.3 x 10(-5) W K-2 m(-1) at 660 K.