The chemical mismatch method has been utilized to screen for mutations in the apoC-II gene of a patient with familial chylomicronemia and apoC-II deficiency. Cleavage of heteroduplexes formed between normal and patient DNA strands with hydroxylamine and osmium tetroxide readily localized a mutation near base 2660 of the mutant apoC-II. Sequence analysis of PCR amplified patient DNA in the mismatched region localized by this method identified the substitution of a thymidine (T) for a cytosine (C) at base 2668 in exon 2 of the patient's gene within a CpG dinucleotide. The C to T transition in the apoC-IIParis2 gene leads to the introduction of a premature termination codon (TGA) at a position corresponding to amino acid-19 of the signal peptide of apoC-II and the formation of a new Nla III restriction enzyme site absent in the normal apoC-II gene. Consistent with the history of consanguinity in this kindred, amplification of DNA isolated from the proband's parents by the polymerase chain reaction and digestion with Nla III established that the proband is a true homozygote for this genetic defect. Analysis of the patient's plasma by two-dimensional gel electrophoresis and immunoblotting failed to detect any plasma apoC-II. Thus, we have identified a novel mutation in the apoC-II gene of a patient with apoC-II deficiency from a Paris kindred presenting with severe hypertriglyceridemia and chylomicronemia.(ABSTRACT TRUNCATED AT 250 WORDS)