To study the effects of AD mutations in APP and PSEN1 on the neuronal endolysosomal system, we generated cortical excitatory neurons from iPSCs derived from individuals with genetic changes or mutations causal for AD: APP V717I, trisomy chromosome 21 (Ts21), APP duplication (APPdup), and three different PSEN1 mutations (Y115C, M146I, and Intron 4). Here, APP is linked to Alzheimer disease.