In this study we identified and independently replicated a novel association between a variant in the FRMPD1 gene and HIV acquisition. The magnitude of the replicable association between this newly implicated SNP (rs4878712) and HIV acquisition is modest. Nonetheless, the potential pathway we present (rs4878712 to FBXO10 and FBXO10 to BCL2/Bcl-2) has good biological plausibility, given the observed protection against viral replication and lower level of infectivity in vitro due to basal level of Bcl-2. This or other pathways associated with rs4878712 could be important mechanisms contributing to the variability in susceptibility to HIV infection upon exposure and provide new targets for medication development.