Nuclear pore complexes (NPCs) are established players in cell division and differentiation. However studies on the contribution of individual NPC subunits to these processes are still scarce. Here we use mouse embryonic stem cells (mESCs) to characterize the role of NPC structural components, focusing on the short arm of the Y-complex that comprises Nup85, Seh1 and Nup43. We show that Seh1 and Nup43, although dispensable at the pluripotent stage, are required for normal cell growth rates, and for mESC viability upon differentiation. mESCs lacking Seh1 or Nup43 display a mild reduction of NPC density that is also observed in an N-terminally truncated Nup85 mutant in which interaction with Seh1 is greatly impaired. However, mESC proliferation and differentiation are not altered in these Nup85 mutant cells, indicating that it is the integrity of the Y-complex, rather than the number of NPCs, that is critical to ensure these processes.