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Genetic variants resulting in non-expression of complement  C4A  and  C4B  genes are common in healthy European populations and have shown association with a number of diseases, most notably the autoimmune disease, systemic lupus erythematosus. The most frequent cause of a  C4  “null” allele, following that of  C4  gene copy number variation (CNV), is a non-sense mutation arising from a 2 bp CT insertion into codon 1232 of exon 29. Previous attempts to accurately genotype this polymorphism have not been amenable to high-throughput typing, and have been confounded by failure to account for CNV at this locus, as well as by inability to distinguish between paralogs. We have developed a novel, high-throughput, paralog-specific assay to detect the presence and copy number of this polymorphism. We have genotyped healthy cohorts from the United Kingdom (UK) and Spain. Overall, 30/719 (4.17%) individuals from the UK cohort and 8/449 (1.78%) individuals from the Spanish cohort harboured the CT insertion in a  C4A  gene. A single Spanish individual possessed a  C4B  CT insertion. There is weak correlation between the  C4  CT insertion and flanking MHC polymorphism. Therefore it is important to note that, as with  C4  gene CNV, disease-association due to this variant will be missed by current SNP-based genome-wide association strategies.

Determination of the Loss of Function Complement C4 Exon 29 CT Insertion Using a Novel Paralog-Specific Assay in Healthy UK and Spanish Populations