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Targeted sequencing of <jats:italic>ABCA7<\/jats:italic> suggests a role for rare premature termination codon (PTC) mutations in AD, with haploinsufficiency through nonsense-mediated mRNA decay as a plausible pathogenic mechanism. Since other classes of rare variants in <jats:italic>ABCA7<\/jats:italic> are poorly understood, we investigated the contribution and pathogenicity of rare missense, indel and splice variants in <jats:italic>ABCA7<\/jats:italic> in Belgian AD patient and control cohorts. We identified 8.36% rare variants in the patient cohort versus 6.05% in the control cohort. For 10 missense mutations identified in the Belgian cohort we analyzed the pathogenetic effect on protein localization in vitro using immunocytochemistry. Our results demonstrate that rare <jats:italic>ABCA7<\/jats:italic> missense mutations can contribute to AD by inducing protein mislocalization, resulting in a lack of functional protein at the plasma membrane. In one pedigree, a mislocalization-inducing missense mutation in <jats:italic>ABCA7<\/jats:italic> (p.G1820S) co-segregated with AD in an autosomal dominant inheritance pattern. Brain autopsy of six patient missense mutation carriers showed typical AD neuropathological characteristics including cerebral amyloid angiopathy type 1. Also, among the rare <jats:italic>ABCA7<\/jats:italic> missense mutations, we observed mutations that affect amino acid residues that are conserved in ABCA1 and ABCA4, of which some correspond to established <jats:italic>ABCA1<\/jats:italic> or <jats:italic>ABCA4<\/jats:italic> disease-causing mutations involved in Tangier or Stargardt disease.<\/jats:p>","DOI":"10.1186\/s40478-022-01346-3","type":"journal-article","created":{"date-parts":[[2022,3,31]],"date-time":"2022-03-31T20:04:57Z","timestamp":1648757097000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["Rare missense mutations in ABCA7 might increase Alzheimer\u2019s disease risk by plasma membrane exclusion"],"prefix":"10.1186","volume":"10","author":[{"given":"Liene","family":"Bossaerts","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elisabeth","family":"Hendrickx Van de Craen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rita","family":"Cacace","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bob","family":"Asselbergh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christine","family":"Van Broeckhoven","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2022,3,31]]},"reference":[{"issue":"3","key":"1346_CR1","doi-asserted-by":"crossref","first-page":"e79","DOI":"10.1212\/NXG.0000000000000079","volume":"2","author":"HN Cukier","year":"2016","unstructured":"Cukier HN et al (2016) ABCA7 frameshift deletion associated with Alzheimer disease in African Americans. 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