The molecular defects in the lecithin:cholesterol acyltransferase (LCAT) gene have been identified in a 52-year-old patient with classic LCAT deficiency, presenting with corneal clouding and proteinuria. Plasma total cholesterol was normal, triglycerides were elevated, whereas high density lipoprotein (HDL) cholesterol (8 mg/dl) and plasma cholesteryl esters (6% of total cholesterol) were markedly reduced. Plasma cholesterol esterification rate (pCER) was zero, alpha-LCAT activity, assayed using an HDL-like proteoliposome substrate was reduced to 1.6% of control, and LCAT mass was 3.7% of normal plasma levels. DNA sequence analysis of the proband's LCAT gene identified a C to A substitution, converting tyr83 to a stop codon, and a T to A transition, replacing tyr156 by asn. Restriction analysis of PCR-amplified DNA from the proband, a control and his four children using the enzymes Acc I and Rsa I established that the patient is a compound heterozygote for both mutations. The two children, heterozygous for the stop codon defect, were phenotypically indistinguishable from the two with the tyr156 defect. In vitro expression of LCAT (tyr156-->asn) in human embryonic kidney-293 cells established the functional significance of this mutation. The secreted translation product had only 6% of control mass and no detectable CER; however, the residual LCAT mass of the in vitro expressed LCAT (tyr156-->asn) demonstrated a specific alpha-LCAT activity of 30% of control, suggesting that this amino acid substitution results in a mutant enzyme that retains some enzymic activity, but may be rapidly catabolized. In summary, we have identified two unique defects in the LCAT gene that lead to the expression of classic LCAT deficiency in this kindred.