A first clathrate compound with selenium guest atoms, [Ge(46-x)P(x)]Se(8-y)□(y) (x = 15.4(1); y = 0-2.65; □ denotes a vacancy), was synthesized as a single-phase and structurally characterized. It crystallizes in the space group Fm3 with the unit cell parameter a varying from 20.310(2) to 20.406(2) Å and corresponding to a 2 × 2 × 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, [Ge(46-x)P(x)]Se(8-y)□(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 × 10(-5) W K(-2) m(-1) at 660 K.