In the discovery stage of a large family-based GWAS assessing low-frequency (MAF≤5%) variants in late-onset Alzheimer’s disease an intronic SNP in PLXNA4 (rs277484, MAF = 2.0% in 1000genomes) yielded the most significant association signal (p = 9.0×10−10). This evidence concerns the gene PLXNA4 and early-onset autosomal dominant Alzheimer disease.