Mutations in NCF1 encodes phagocytic nicotinamide adenine phosphate (NADPH) p47-phox protein, which accounts for 23% of chronic granulomatous disease (CGD), a rare inherited inborn error of immunity (IEI). NCF1 has 2 pseudogenes near its chromosomal locus 7q11.23. Reciprocal crossover between functional genes and pseudogenes in high frequency can obscure DNA interpretation, thereby complicating diagnosis, especially in atypical presentations.
A 4-year-old male from Saudi Arabia with recurrent Rhizopus skin infections had oxidative burst assay with a broad peak of intermediate granulocyte dihydrorhodamine (DHR) fluorescence and an abnormal population, suggesting AR CGD. Genetic CGD panel identified no variants in known CGD genes. Gene ratios revealed his defect was not found in the common ΔGT region at the start of exon 2. The variant found in NCF1 was c.579 G>A, p. Trp193X, a previously reported pathogenic variant in the NCF1 gene. Western blot showed absent p47 protein, thus confirming NCF1-deficient CGD.
A 5-year-old female with a history of congenital heart block and recurrent mucosal aphthous ulcers presented with recurrent fevers. Labs showed low NK counts and elevated sIL-2 receptor but normal lymphocyte counts, immunoglobulins, cytokines, and CXCL9. Lip biopsy suggested orofacial Crohn disease. Whole-exome sequencing was negative. Neutrophil oxidative burst assay showed normal and abnormal granulocyte DHR fluorescence populations of stimulated granulocytes, suggesting the carrier state of CGD. Genetic testing and flow confirmed a ΔGT deletion in p47phox/NCF1 gene.
Mutations in genes encoding components of phagocyte NADPH oxidase manifests as CGD. Dinucleotide deletion in NCF1 exon 2 pseudogenes leads to frameshift alterations. This can cause premature stop codons, which replace authentic NCF1. This variation in the ratio of functional genes to pseudogenes can result in masking of CGD on routine testing. Non-ΔGT mutations occur in ∼20% of p47phox patients. Sanger sequencing is sometimes not sufficient to determine the underlying defect in NCF1 due to the extensive sequence homology of NCF1 with pseudogenes. With atypical presentations of CGD as described here, a high index of suspicion is needed in order to broaden workup when evaluating patients with clinical manifestations that suggest possible IEI.
