We have previously reported an 8-year-old girl with lipoprotein glomerulopathy. Assessment of serum apolipoprotein E (apo E) in this patient showed a discrepancy between phenotype and genotype, suggesting that she may have a variant of apo E. The present report concerns our analysis of DNA sequences of the apo E gene in the patient: nine base pairs were found to be deleted from exon 4. This mutation would appear to encode a new apo E variant lacking three amino acids. This variant may be associated with the pathogenesis of lipoprotein glomerulopathy.