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The low-density lipoprotein (LDL) receptor plays a central role in uptake and clearance of LDL cholesterol. Using whole-genome sequence data from 43,202 Icelanders, we searched for deletions in the LDL receptor gene (LDLR) using a recently developed paired-read based algorithm. We identified a 2.7 kilobase deletion involving the 3’ untranslated region (3’-UTR) of LDLR that was present in four closely related individuals. Three carriers with available lipid measurements have very low mean levels of LDL cholesterol: 0.55, 1.01 and 1.19 mmol/L, respectively. This translates to 72% lower mean LDL cholesterol than in non-carriers (0.92 vs. 3.3 mmol/L [35.5 vs. 127.4 mg/dL], respectively; P = 3.1 х 10^-6; total sample of 87,788 individuals, SD = 0.90 mmol/L). Mean levels of HDL cholesterol and triglycerides are within normal range. Three of the carriers are alive at ages 33 to 60 and apparently healthy, the fourth …