Rare variants in APP, PSEN1 and PSEN2 increase risk for AD in late-onset Alzheimer’s disease families
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Pathogenic mutations in APP, PSEN1, PSEN2, MAPT and GRN have previously been linked to familial early onset forms of dementia. Mutation screening in these genes has been performed in either very small series or in single families with late onset AD (LOAD). Similarly, studies in single families have reported mutations in MAPT and GRN associated with clinical AD but no systematic screen of a large dataset has been performed to determine how frequently this occurs. We report sequence data for 439 probands from late-onset AD families with a history of four or more affected individuals. Sixty sequenced individuals (13.7%) carried a novel or pathogenic mutation. Eight pathogenic variants, (one each in APP and MAPT, two in PSEN1 and four in GRN) three of which are novel, were found in 14 samples. Thirteen additional variants, present in 23 families, did not segregate with disease, but the frequency of these variants is higher in AD cases than controls, indicating that these variants may also modify risk for disease. The frequency of rare variants in these genes in this series is significantly higher than in the 1,000 genome project (p = 5.09 × 10⁻⁵; OR = 2.21; 95%CI = 1.49-3.28) or an unselected population of 12,481 samples (p = 6.82 × 10⁻⁵; OR = 2.19; 95%CI = 1.347-3.26). Rare coding variants in APP, PSEN1 and PSEN2, increase risk for or cause late onset AD. The presence of variants in these genes in LOAD and early-onset AD demonstrates that factors other than the mutation can impact the age at onset and penetrance of at least some variants associated with AD. MAPT and GRN mutations can be found in clinical series of AD most likely due to misdiagnosis. This study clearly demonstrates that rare variants in these genes could explain an important proportion of genetic heritability of AD, which is not detected by GWAS.
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Rare variants in genes associated with Alzheimer disease pathogenesis could explain a significant proportion of the genetic heritability of Alzheimer disease that is not detected by genome-wide association studies.
“suggesting that rare variants in genes associated with AD pathogenesis could explain a significant proportion of genetic heritability of AD, which is not detected by genomewide association studies (53)”
From Molecular Basis for Increased Risk for Late-onset Alzheimer Disease Due to the Naturally Occurring L28P Mutation in Apolipoprotein E4 (2014) · cites this paper as [53]
Rare variants in amyloid beta precursor protein, presenilin 1, and presenilin 2 increased the risk for Alzheimer disease in late-onset Alzheimer disease families.
“A characteristic example involves a mutation screening study that showed that rare variants in amyloid  precursor protein, presenilin 1, and presenilin 2 increased the risk for AD in LOAD families, suggesting that rare variants in genes associated with AD pathogenesis could explain a significant proportion of genetic heritability of AD, which is not detected by genomewide association studies (53)”
From Molecular Basis for Increased Risk for Late-onset Alzheimer Disease Due to the Naturally Occurring L28P Mutation in Apolipoprotein E4 (2014) · cites this paper as [53]
Sequencing studies have identified rare variants in APP, PSEN1, and PSEN2 that increase risk for LOAD.
“In support, sequencing studies have identified rare variants in APP, PSEN1, and PSEN2 that increase risk for LOAD [157].”
From Genetic architecture of Alzheimer's disease (2020) · cites this paper as [157]
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“Given the overlap between EOAD and LOAD as discussed above, these modifiers may provide potential therapeutic targets for a more general population.”
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Alzheimer’s as a Systems-Level Disease Involving the Interplay of Multiple Cellular Networks
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McKay, N. S., Gordon, B. A., Hornbeck, R. C., Dincer, A., Flores, S. E., Keefe, S., Joseph‐Mathurin, N., Jack, C. R., Koeppe, R. A., Millar, P. R., et al. (2023) · Nature Neuroscience · doi:10.1038/s41593-023-01359-8 · Cited by 43 · see citing works
Self-citationDisease‐related mutations among Caribbean Hispanics with familial dementia
Lee, J. H., Kahn, A., Cheng, R., Reitz, C., Vardarajan, B. N., Lantigua, R., Medrano, M. Z., Jiménez‐Velázquez, I. Z., Williamson, J., Nagy, P. L., et al. (2014) · Molecular Genetics & Genomic Medicine · doi:10.1002/mgg3.85 · Cited by 43 · see citing works
Self-citation
- Authors
- Cruchaga, C., Chakraverty, S., Mayo, K., Vallania, F. L. M., Mitra, R. D., Faber, K., Williamson, J., Bird, T., Diaz-Arrastia, R., Foroud, T. M., Boeve, B. F., Graff-Radford, N. R., St. Jean, P., Lawson, M., Ehm, M. G., Mayeux, R., Goate, A. M., & for the NIA-LOAD/NCRAD Family Study Consortium
- Affiliations
- Washington University in St. Louis (US)
- Indiana University Indianapolis (US)
- Columbia University (US)
- University of Washington (US)
- The University of Texas Southwestern Medical Center (US)
- Mayo Clinic (US)
- GlaxoSmithKline (United States) (US)
- Corresponding author
- Cruchaga, Carlos
- Goate, Alison M.
- ORCID
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-02-01
- Volume
- 7
- Issue
- 2
- Pages
- e31039
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3270040
- OpenAlex
- W2023381648
- Cited by
- 320
- References
- 66
- Citations by year
- 2026: 15 · 2025: 14 · 2024: 23 · 2023: 12 · 2022: 20 · 2021: 25 · 2020: 25 · 2019: 10 · 2018: 22 · 2017: 28 · 2016: 26 · 2015: 22 · 2014: 29 · 2013: 32 · 2012: 17
- FWCI
- 21.43
- Type
- journal article
- Language
- en
- Update notices
- correction (2012-05-10)
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- U.S. Department of Veterans Affairs
- Massachusetts General Hospital
- University of Southern California
- University of Pennsylvania (U24 AG026395)
- Northwestern University
- Foundation for Barnes-Jewish Hospital
- University of Washington
- University of Pittsburgh
- Rush University
- National Institutes of Health (5p30ns069329-02, 5r37ag015473-15)
- University of California, Los Angeles
- National Institute on Aging (AG 16208, R37AG15473, R37-AG015473, AG21886, R01AG035083, U24 AG21886, P 50 AG05681, R01AG041797, P50AG008702, P50AG005681, P01 AG0 3991, P01AG003991, AG035083, U24AG026395, P30AG013846, R01AG016208, AG026395, U24AG056270, P01AG026276, U24AG021886)
- National Institute of Mental Health (R01MH060009)
- National Institute of Neurological Disorders and Stroke (P30-NS069329, 1P30NS069329-01)
- Topics
- Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
- Health Sciences › Medicine › Psychiatry and Mental health › Dementia and Cognitive Impairment Research
- Health Sciences › Medicine › Neurology › Amyotrophic Lateral Sclerosis Research
- Keywords
- late-onset Alzheimer's disease, familial Alzheimer's disease, rare variants, APP, presenilin 1, presenilin 2, MAPT, gene regulatory networks, pathogenic variants, genetic risk, heritability, novel variants, age of onset, penetrance, misdiagnosis, mutation detection
- MeSH terms
- Progranulins, Adult, Aged, Aged, 80 and over, Alzheimer Disease, Female, Humans, Male, Middle Aged, Mutation, Pedigree, Amyloid beta-Protein Precursor, tau Proteins, Genetic Predisposition to Disease, Intercellular Signaling Peptides and Proteins, Presenilin-1, Presenilin-2
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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