The molecular mechanism of C3 deficiency in an Afrikaans patient with recurrent pyogenic infections was studied. Restriction enzyme analysis showed a gene deletion of 800 base pairs (bp) mapping to the a chain of C3. Amplification of genomic DNA, using the PCR, demonstrated that the deletion included exons 22 and 23 of the C3 gene. Truncated mRNA was shown in an Epstein-Barr virus-transformed B-cell line by PCR amplification of first-strand cDNA. A consequence of this deletion was that the RNA transcribed 3' to the deletion was out of frame, resulting in formation of a stop codon 19 bp downstream from the deletion. The molecular basis of the deletion was compatible with homologous recombination between two Alu sequences located in introns 21 and 23. An unrelated nonconsanguineous relative and two of a sample of 174 Afrikaansspeaking individuals were heterozygous carriers of the same gene deletion. The wide prevalence of this null allele in this population is probably due to the effects of a small founder population. The presence of this deletion in the C3 gene is not compatible with production ofany functional C3, supporting the idea that study of such patients offers a valid model for understanding physiological activities of C3 in vivo in humans.Analysis of patients with hereditary deficiencies of complement proteins has given insight into the physiological actions in vivo of the complement system in host defense against pyogenic infections and disease mediated by immune complexes. Complement protein C3 is the major protein of the complement system in plasma in terms of quantitative expression, at -1 g/liter. Cleavage of C3 by C3 convertase enzymes results in release of the anaphylatoxin C3a. The other product of the initial cleavage of C3, C3b, covalently fixed to surfaces, acts as a focus for formation of the C5 convertase enzyme and, together with its further cleavage product, iC3b, is a ligand for complement receptors CR1 and CR3. Absence of C3 is a rare condition in humans and provides the best opportunity for investigating the physiological activities of this protein in vivo in humans.To date 15 patients, who suffered from recurrent pyogenic infections and/or rashes and nephritis (1-10), have been described with inherited homozygous C3 deficiency. Characterization of the full genomic organization of the human C3 gene (11) allowed us to identify a splice site mutation as the molecular basis for C3 deficiency in a 10-year-old English patient (12).