In summary, our study identifies biochemical and immunocytochemical interactions between LRRTM3, BACE1 and APP; gene expression correlations between these genes and also CTNNA3; confirms the effect of LRRTM3 siRNA on reducing BACE1-cleavage products of APP and detects MLGs in the 5′UTR-Intron 1 region of LRRTM3 that associate with AD risk. This evidence concerns the gene LRRTM3 and Alzheimer disease.