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ObjectiveSynonymous variants can lead to disease; nevertheless, the majority of sequencing studies conducted in Alzheimer disease (AD) only assessed coding variation.MethodsTo detect synonymous variants modulating AD risk, we conducted a whole-genome sequencing study on 67 Caribbean Hispanic (CH) families multiply affected by AD. Identified disease-associated variants were further assessed in an independent cohort of CHs, expression quantitative trait locus (eQTL) data, brain autopsy data, and functional experiments.ResultsRare synonymous variants in 4 genes (CDH23, SLC9A3R1, RHBDD2,andITIH2) segregated with AD status in multiplex families and had a significantly higher frequency in these families compared with reference populations of similar ancestry. In comparison to subjects without dementia, expression ofCDH23(β = 0.53,p= 0.006) andSLC9A3R1(β = 0.50,p= 0.02) was increased, and expression ofRHBDD2(β = −0.70,p= 0.02) decreased in individuals with AD at death. In line with this finding, increased expression ofCDH23(β = 0.26 ± 0.08,p= 4.9E-4) and decreased expression ofRHBDD2(β = −0.60 ± 0.12,p= 5.5E-7) were related to brain amyloid load (p= 0.0025).SLC9A3R1expression was associated with burden of TDP43 pathology (β = 0.58 ± 0.17,p= 5.9E-4). Using eQTL data, theCDH23variant was in linkage disequilibrium with variants modulatingCDH23expression levels (top single nucleotide polymorphism: rs11000035,p= 4.85E-6, D' = 1.0). Using minigene splicing assays, theCDH23andSLC9A3R1variants affected splicing efficiency.ConclusionsThese findings suggest thatCDH23, SLC9A3R1, RHBDD2, and possiblyITIH2, which are involved in synaptic function, the glutamatergic system, and innate immunity, contribute to AD etiology. In addition, this study supports the notion that synonymous variants contribute to AD risk and that comprehensive scrutinization of this type of genetic variation is warranted and critical.