Genome-wide association studies (GWAS) have identified several risk variants for late-onset Alzheimer's disease (LOAD). These common variants have replicable but small effects on LOAD risk and generally do not have obvious functional effects. Low-frequency coding variants, not detected by GWAS, are predicted to include functional variants with larger effects on risk. To identify low-frequency coding variants with large effects on LOAD risk, we carried out whole-exome sequencing (WES) in 14 large LOAD families and follow-up analyses of the candidate variants in several large LOAD case-control data sets. A rare variant in PLD3 (phospholipase D3; Val232Met) segregated with disease status in two independent families and doubled risk for Alzheimer's disease in seven independent case-control series with a total of more than 11,000 cases and controls of European descent. Gene-based burden analyses in 4,387 cases and controls of European descent and 302 African American cases and controls, with complete sequence data for PLD3, reveal that several variants in this gene increase risk for Alzheimer's disease in both populations. PLD3 is highly expressed in brain regions that are vulnerable to Alzheimer's disease pathology, including hippocampus and cortex, and is expressed at significantly lower levels in neurons from Alzheimer's disease brains compared to control brains. Overexpression of PLD3 leads to a significant decrease in intracellular amyloid-beta precursor protein (APP) and extracellular Abeta42 and Abeta40 (the 42- and 40-residue isoforms of the amyloid-beta peptide), and knockdown of PLD3 leads to a significant increase in extracellular Abeta42 and Abeta40. Together, our genetic and functional data indicate that carriers of PLD3 coding variants have a twofold increased risk for LOAD and that PLD3 influences APP processing. This study provides an example of how densely affected families may help to identify rare variants with large effects on risk for disease or other complex traits. ; Cruchaga, Carlos Karch, Celeste M Jin, Sheng Chih Benitez, Bruno A Cai, Yefei Guerreiro, Rita Harari, Oscar Norton, Joanne Budde, John Bertelsen, Sarah Jeng, Amanda T Cooper, Breanna Skorupa, Tara Carrell, David Levitch, Denise Hsu, Simon Choi, Jiyoon Ryten, Mina Hardy, John Trabzuni, Daniah Weale, Michael E Ramasamy, Adaikalavan Smith, Colin Sassi, Celeste Bras, Jose Gibbs, J Raphael Hernandez, Dena G Lupton, Michelle K Powell, John Forabosco, Paola Ridge, Perry G Corcoran, Christopher D Tschanz, Joann T Norton, Maria C Munger, Ronald G Schmutz, Cameron Leary, Maegan Demirci, F Yesim Bamne, Mikhil N Wang, Xingbin Lopez, Oscar L Ganguli, Mary Medway, Christopher Turton, James Lord, Jenny Braae, Anne Barber, Imelda Brown, Kristelle Passmore, Peter Craig, David Johnston, Janet McGuinness, Bernadette Todd, Stephen Heun, Reinhard Kolsch, Heike Kehoe, Patrick G Hooper, Nigel M Vardy, Emma R L C Mann, David M Pickering-Brown, Stuart Kalsheker, Noor Lowe, James Morgan, Kevin David Smith, A Wilcock, Gordon Warden, Donald Holmes, Clive Pastor, Pau Lorenzo-Betancor, Oswaldo Brkanac, Zoran Scott, Erick Topol, Eric Rogaeva, Ekaterina Singleton, Andrew B Kamboh, M Ilyas St George-Hyslop, Peter Cairns, Nigel Morris, John C Kauwe, John S K Goate, Alison M 089698/Wellcome Trust/United Kingdom 089703/Wellcome Trust/United Kingdom 100140/Wellcome Trust/United Kingdom 1R01AG041797/AG/NIA NIH HHS/ 5U24AG026395/AG/NIA NIH HHS/ AG005133/AG/NIA NIH HHS/ AG023652/AG/NIA NIH HHS/ AG030653/AG/NIA NIH HHS/ AG041718/AG/NIA NIH HHS/ AG07562/AG/NIA NIH HHS/ G0802462/Medical Research Council/United Kingdom G0901254/Medical Research Council/United Kingdom NIH P50 AG05681/AG/NIA NIH HHS/ NIH R01039700/PHS HHS/ P01 AG003991/AG/NIA NIH HHS/ P01 AG026276/AG/NIA NIH HHS/ P01 AG03991/AG/NIA NIH HHS/ P30 NS069329/NS/NINDS NIH HHS/ P30-NS069329/NS/NINDS NIH HHS/ P50 AG005133/AG/NIA NIH HHS/ P50 AG005681/AG/NIA NIH HHS/ R01 AG011380/AG/NIA NIH HHS/ R01 AG030653/AG/NIA NIH HHS/ R01 AG035083/AG/NIA NIH HHS/ R01 AG039700/AG/NIA NIH HHS/ R01 AG041718/AG/NIA NIH HHS/ R01 AG041797/AG/NIA NIH HHS/ R01 AG042611/AG/NIA NIH HHS/ R01 AG044546/AG/NIA NIH HHS/ R01-AG035083/AG/NIA NIH HHS/ R01-AG042611/AG/NIA NIH HHS/ R01-AG044546/AG/NIA NIH HHS/ R01-AG11380/AG/NIA NIH HHS/ R01-AG18712/AG/NIA NIH HHS/ R01-AG21136/AG/NIA NIH HHS/ R01AG21136/AG/NIA NIH HHS/ R25 DA027995/DA/NIDA NIH HHS/ U24 AG021886/AG/NIA NIH HHS/ U24 AG026395/AG/NIA NIH HHS/ U24AG21886/AG/NIA NIH HHS/ WT089698/Wellcome Trust/United Kingdom ZIA AG000950-11/AG/NIA NIH HHS/ ZO1 AG000950-10/AG/NIA NIH HHS/ ZO1AG000950-11/AG/NIA NIH HHS/ Canadian Institutes of Health Research/Canada England Nature. 2014 Jan 23;505(7484):550-4. doi: 10.1038/nature12825. Epub 2013 Dec 11.