A new apolipoprotein E (apo E) phenotype has been demonstrated in a Finnish hypertriglyceridemic subject (R.M.). At the time of this study, R.M.'s plasma triglyceride and cholesterol levels were 1,021 and 230 mg/dl, respectively. The subject's apo E isoelectric focusing pattern was characterized by two major bands, one in the E3 position and the other in the E1 position. Normally the E1 position is occupied by sialylated derivatives of apo E4, E3, or E2. The E1 band of subject R.M. is not a sialylated form, however, because it was not affected by neuraminidase digestion. The identity of the E1 variant as a genetically determined structure was established by amino acid and partial sequence analyses, confirming that the variant is an example of a previously uncharacterized apo E phenotype, E3/1. Both cysteamine modification and amino acid analysis demonstrated that this variant contains two cysteine residues per mole. Sequence analysis of two cyanogen bromide fragments and one tryptic fragment of the apo E3/1 showed that it differs from E2(Arg158----Cys) at residue 127, where an aspartic acid residue is substituted for glycine. This single amino acid interchange is sufficient to account for the one-charge difference observed on isoelectric focusing gels between E2(Arg158----Cys) and the E1 variant. The variant has been designated E1 (Gly127----Asp, Arg158----Cys). When compared with apo E3, the E1 variant demonstrated reduced ability to compete with 125I-LDL for binding to LDL (apo B,E) receptors on cultured fibroblasts (approximately 4% of the amount of binding of apo E3). This defective binding is similar to that of E2-(Arg158----Cys). Therefore, the binding defect of the variant is probably due to the presence of cysteine at residue 158, rather than aspartic acid at residue 127. In contrast, the apo E3 isoform from this subject demonstrated normal binding activity, indicating that it has a normal structure. In family studies, the vertical transmission of the apo E1 variant has been established. It is not yet clear, however, if the hypertriglyceridemia observed in the proband is associated with the presence of the E1(Gly127----Asp, Arg158----Cys) variant.