Rare damaging variants in genes encoding the phospholipid transporters ATP8B4 and ABCA1 have been identified as risk factors for Alzheimer disease (AD). Exome sequencing was performed in 16,036 individuals with AD and 16,522 control individuals. The known risk genes TREM2, SORL1 and ABCA7 were also confirmed to be associated with AD risk. The newly identified genes support the involvement of lipid metabolism and microglial function in AD pathology.