Non-coding cis-regulatory variants in HK1 cause congenital hyperinsulinism with variable disease severity
Authors: Jasmin J. Bennett, Cécile Saint-Martin, Bianca Neumann, Jonna M. E. Männistö, Jayne A. L. Houghton, Susann Empting, Matthew B. Johnson, Thomas W. Laver, Jonathan M. Locke, Benjamin Spurrier, Matthew N. Wakeling, Indraneel Banerjee, Antonia Dastamani, Hüseyin Demirbilek, John Mitchell, Markus Stange, Marie-Thérèse Abi Warde, Mehta Amrita, Romy Aravena, Alina Arion, Navoda Atapattu, Ivo Barić, Jérôme Bertherat, Esra Bilici, Juliette Bouchereau, Karine Braun, Marie-Neige Campas-Lebecque, Mireille Castanet, Catie Cessans, Louise S. Conwell, Preeti Dabadghao, Archana Dayal Arya, Pascale de Lonlay, Liat de Vries, Céline Droumaguet, Noémie Faure-Galon, Olivier Gilly, Alice Goldenberg, Anne-Sophie Guemann, Anne-Marie Guerrot, Julie Harvengt, Samar S. Hassan, Saw Shi Hui, Khadija Nuzhat Humayun, M. Ibrahim, Vandana Jain, Dhivyalakshmi Jeevarathnam, Kah Yin Loke, Vaman Khadilkar, I. P. S. Kochar, Abhishek Kulkarni, Aniket Kumbhojkar, Delphine Lamireau, Floris Levy-Khademi, Catarina Limbert, Martin Lindner, Catherine Lombard, François Maillot, Karine Mention, Verónica Mericq, Zainaba Mohamed, Coline Mornet, Philip Murray, Alexandre Naccache, Lusine V. Navasardyan, Kristen Neville, Ramona Nicolescu, Marc Nicolino, Elisa Nishimura-Meguro, Nattakarn Numsriskulrat, Sinead O’sullivan, Yasmine Ouarezki, Armelle Pambou, Florence Petit, V. P. Praveen, Mélanie Priou-Guesdon, Stoeva Radka, Birgit Rami-Merhar, Sudha Rao, Yves Reznik, Laurence Rulquin, Maria Salomon Estebanez, Isabelle Souto, Antoine Tabarin, Ana Tangari, Sara Van Aken, Charles Verge, Hélène Vinolas, Christel Voinot, Robert Wagner, Jan Walker, Esko Wiltshire, Klaus Mohnike, Jean-Baptiste Arnoux, Nick D. L. Owens, Martin Zenker, Christine Bellanné-Chantelot, Sarah E. Flanagan
Journal: Genome Medicine (2025)

We recently reported non-coding variants in a cis-regulatory element of the beta-cell disallowed gene hexokinase 1 (HK1) as a novel cause of congenital hyperinsulinism. These variants lead to a loss of repression of HK1 in pancreatic beta-cells, causing insulin secretion during hypoglycaemia. In this study, we aimed to determine the prevalence, genetics, and phenotype of HK1-hyperinsulinism by screening a large international cohort of patients living with the condition. We screened the HK1 cis-regulatory region in 1761 probands with hyperinsulinism of unknown aetiology who had been referred to one of three large European genomics laboratories. We identified a HK1 variant in 89/1761 probands (5%) and 63 family members. Within the Exeter HI cohort, these variants accounted for 2.8% of all positive genetic diagnoses (n = 54/1913) establishing this as an important cause of HI. Individuals with a disease-causing variant were diagnosed with hyperinsulinism between birth and 26 years (median: 7 days) with variable response to treatment; 80% were medically managed and 20% underwent pancreatic surgery due to poor response to medical therapy. Glycaemic outcomes varied from spontaneous remission to hypoglycaemia persisting into adulthood. Eight probands had inherited the variant from a parent not reported to have hyperinsulinism (median current age: 39 years), confirming variable penetrance. Two of the 23 novel HK1 variants allowed us to extend the minimal cis-regulatory region from 42 to 46 bp. Non-coding variants within the HK1 cis-regulatory region cause hyperinsulinism of variable severity ranging from neonatal-onset, treatment-resistant disease to being asymptomatic into adulthood. Discovering variants in 89 families confirms HK1 as a major cause of hyperinsulinism and highlights the important role of the non-coding genome in human monogenic disease.