title: Identification of a novel NCF-1 (p47-phox) pseudogene not containing the signature GT deletion: significance for A47 degrees chronic granulomatous disease carrier detection.
abstract: The p47-phox gene, NCF-1, has 2 nearly identical pseudogenes (psiNCF-1) in proximity at chromosomal locus 7q11.23. A dinucleotide deletion (DeltaGT) 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 degrees ) chronic granulomatous disease (CGD) as a result of the insertion of a DeltaGT-containing fragment of pseudogene into NCF-1. Extending our study of the relationship between NCF-1 and psiNCF-1 to 53 unaffected control individuals, we found that although in most (n = 44), the ratio of pseudogene (DeltaGT) 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 DeltaGT. It is possible that this pseudogene has not undergone deletion of GT, but more likely, based on analysis of additional NCF-1/psiNCF-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 degrees CGD allele. The existence of 2 extended haplotypes encompassing NCF-1/psiNCF-1 further complicates the detection of A47 degrees CGD carriers. Although most have a DeltaGT/GTGT ratio of 5:1, some have a ratio of 2:1 and are indistinguishable by this means from unaffected individuals.
authors.affiliation: Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA. heyworth@scripps.edu
authors.forename: Paul G
authors.initials: PG
authors.lastname: Heyworth
authors.forename: Deborah
authors.initials: D
authors.lastname: Noack
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Cross
mesh_terms: D002897:Chromosomes, Human, Pair 7; D015894:Genome, Human; D006105:Granulomatous Disease, Chronic / Q000235:genetics*; D006579:Heterozygote; D006801:Humans; D019255:NADPH Oxidases; D010750:Phosphoproteins / Q000235:genetics*; D011544:Pseudogenes; D017384:Sequence Deletion
chemical_list: D010750:Phosphoproteins; D019255:NADPH Oxidases; C060505:neutrophil cytosolic factor 1