A rare genetic variant in fibronectin 1 (FN1) protects against APOEε4 in Alzheimer's disease. The study identified 510 rare coding variants in 476 genes in APOEε4 carriers without dementia, with significant enrichment in extracellular matrix (ECM)-related processes. Two genes, FN1 and COL6A2, were prioritized for further study. In an independent cohort of 7185 APOEε4 homozygous carriers, the rs140926439 variant in FN1 was protective against AD (OR=0.29; 95% CI [0.11, 0.78], P=0.014) and delayed age at onset by 3.37 years (95% CI [0.42, 6.32], P=0.025). FN1 and COL6A2 protein levels were increased at the blood–brain barrier (BBB) in APOEε4 carriers with AD. Brain expression of cognitively unaffected homozygous APOEε4 carriers had significantly lower FN1 deposition and less reactive gliosis compared to homozygous APOEε4 carriers with AD, suggesting that FN1 might be a downstream driver of APOEε4-mediated AD-related pathology and cognitive decline. Zebrafish models with loss-of-function (LOF) mutations in fn1b showed reduced gliosis, enhanced gliovascular remodeling, and potentiated microglial response, suggesting that pathological accumulation of FN1 could impair toxic protein clearance, which is ameliorated with FN1 LOF. The study suggests that vascular deposition of FN1 is related to the pathogenicity of APOEε4, and LOF variants in FN1 may reduce APOEε4-related AD risk, providing novel clues to potential therapeutic interventions targeting the ECM to mitigate AD risk. The study also found that FN1 deposition correlates with APOEε4 dosage and that FN1 deposition is different between demented and cognitively unaffected APOEε4 carriers. The results suggest that FN1 is a critical component of APOEε4-mediated development of AD and a yet unknown protective mechanism against the effects of APOEε4/4 genotype suppresses FN1 deposition. The study highlights the importance of ECM components in AD pathology and suggests that targeting the ECM could be a potential therapeutic strategy for AD.A rare genetic variant in fibronectin 1 (FN1) protects against APOEε4 in Alzheimer's disease. The study identified 510 rare coding variants in 476 genes in APOEε4 carriers without dementia, with significant enrichment in extracellular matrix (ECM)-related processes. Two genes, FN1 and COL6A2, were prioritized for further study. In an independent cohort of 7185 APOEε4 homozygous carriers, the rs140926439 variant in FN1 was protective against AD (OR=0.29; 95% CI [0.11, 0.78], P=0.014) and delayed age at onset by 3.37 years (95% CI [0.42, 6.32], P=0.025). FN1 and COL6A2 protein levels were increased at the blood–brain barrier (BBB) in APOEε4 carriers with AD. Brain expression of cognitively unaffected homozygous APOEε4 carriers had significantly lower FN1 deposition and less reactive gliosis compared to homozygous APOEε4 carriers with AD, suggesting that FN1 might be a downstream driver of APOEε4-mediated AD-related pathology and cognitive decline. Zebrafish models with loss-of-function (LOF) mutations in fn1b showed reduced gliosis, enhanced gliovascular remodeling, and potentiated microglial response, suggesting that pathological accumulation of FN1 could impair toxic protein clearance, which is ameliorated with FN1 LOF. The study suggests that vascular deposition of FN1 is related to the pathogenicity of APOEε4, and LOF variants in FN1 may reduce APOEε4-related AD risk, providing novel clues to potential therapeutic interventions targeting the ECM to mitigate AD risk. The study also found that FN1 deposition correlates with APOEε4 dosage and that FN1 deposition is different between demented and cognitively unaffected APOEε4 carriers. The results suggest that FN1 is a critical component of APOEε4-mediated development of AD and a yet unknown protective mechanism against the effects of APOEε4/4 genotype suppresses FN1 deposition. The study highlights the importance of ECM components in AD pathology and suggests that targeting the ECM could be a potential therapeutic strategy for AD.