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Mendelian disorders in glucose-6-phosphate metabolism can present with inflammatory bowel disease (IBD). Using whole genome sequencing we identified a homozygous variant in the glucose-6-phosphatase G6PC3 (c.911dupC; p.Q305fs*82) in an adult patient with congenital neutropenia, lymphopenia and childhood-onset, therapy-refractory Crohn's disease. Since G6PC3 is expressed in several haematopoietic and non-haematopoietic cells it was unclear whether allogeneic stem cell transplantation (HSCT) would benefit this patient with intestinal inflammation. We show that HSCT resolves G6PC3-associated immunodeficiency and the Crohn's disease phenotype. It illustrates how even in adulthood, next generation sequencing can have a significant impact on clinical practice and healthcare utilization in patients with immunodeficiency and monogenic IBD.

Original publication




Journal article


Journal of Crohn's & colitis

Publication Date



Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Nuffield Department of Experimental Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.


Oxford IBD cohort investigators