Identification of a novel NCF-1 (p47-phox) pseudogene not containing the signature GT deletion: significance for A47° chronic granulomatous disease carrier detection

Abstract

The p47-phox gene, NCF-1, has 2 nearly identical pseudogenes (ψNCF-1) in proximity at chromosomal locus 7q11.23. A dinucleotide deletion (ΔGT) at the beginning of exon 2 that leads to a frameshift and premature stop codon is considered the signature sequence of the pseudogenes. It is also the most prevalent mutation in p47-phox–deficient (A47°) chronic granulomatous disease (CGD) as a result of the insertion of a ΔGT-containing fragment of pseudogene into NCF-1.Extending our study of the relationship between NCF-1 andψNCF-1 to 53 unaffected control individuals, we found that although in most (n = 44), the ratio of pseudogene (ΔGT) to functional gene (GTGT) sequence in amplicons spanning exon 2 was 2:1, as previously observed, surprisingly, in 7 persons the ratio was 1:1, and in 2 persons the ratio was 1:2. The lowered ratios are explained by the presence, in a heterozygous or homozygous state, respectively, of a pseudogene that contains GTGT rather than ΔGT. It is possible that this pseudogene has not undergone deletion of GT, but more likely, based on analysis of additional NCF-1/ψNCF-1 markers, it represents the previously unidentified product of the reciprocal crossover of DNA fragments between the functional gene and one of its pseudogenes. The mutated NCF-1 resulting from this event is the predominant A47°CGD allele. The existence of 2 extended haplotypes encompassing NCF-1/ψNCF-1 further complicates the detection of A47°CGD carriers. Although most have a ΔGT/GTGT ratio of 5:1, some have a ratio of 2:1 and are indistinguishable by this means from unaffected individuals.