Systematic analysis of loss-of-function variants across MODY genes demonstrates gene- and NMD-specific effects and identifies NMD-escape INS variants as a novel cause of MODY

Aims/hypothesisAccurate interpretation of loss-of-function (LOF) variants in MODY genes is essential for diagnosis but remains challenging, particularly for variants predicted to escape nonsense-mediated decay (NMD). We aimed to systematically evaluate the pathogenicity of LOF variants, stratified by NMD-triggering and NMD-escape status, across all known MODY genes. MethodsWe analysed ultra-rare LOF variants (minor allele frequency <1 in 10,000) in 5171 individuals of European ancestry with suspected MODY, compared with 155,501 population-based controls from UK Biobank. LOF variants in ABCC8, GCK, HNF1A, HNF4A, HNF1B, INS, KCNJ11, NEUROD1, PDX1, and RFX6 were classified as NMD-triggering or NMD-escape. We tested for gene-level enrichment in cases versus controls. For novel associations, we performed replication in additional MODY cases, assessed familial co-segregation, and undertook in-silico protein modelling. ResultsLOF variants were significantly enriched in all MODY genes except ABCC8 and KCNJ11. Both NMD-triggering and NMD-escape variants were enriched in GCK, HNF1A, and HNF4A, consistent with haploinsufficiency (all P <10-3). HNF1B and RFX6 showed enrichment only for NMD-triggering variants, while NEUROD1 and PDX1 were enriched for only NMD-escape variants. A novel finding was significant enrichment of only NMD-escape LOF variants in INS (OR = 181, P < 10-5). Including replication, we identified eight families with 17 affected individuals carrying INS variants. These variants co-segregated with diabetes (LOD score = 3), included one de novo case, and were absent from >800,000 population controls. Individuals presented with diabetes at a median age of 19 years, had median BMI of 22.9 kg/m2, were negative for islet autoantibodies, and had low type 1 diabetes genetic risk scores. Compared with INS missense MODY, diagnosis occurred [~]10 years later. Protein modelling suggested that INS NMD-escape variants produce aberrant proinsulin molecules with unpaired B chain cysteines, leading to milder misfolding. Conclusions/interpretationThe pathogenicity of LOF variants in MODY genes depends on gene context and NMD status. Heterozygous NMD-escape LOF variants in INS are a novel cause of MODY. These findings provide systematic gene-level evidence to inform variant interpretation guidelines and improve the accuracy of MODY diagnosis in clinical practice. Research in ContextO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIInterpretation of loss-of-function (LOF) variants is complex and strongly influenced by predicted NMD status. C_LIO_LICurrent evidence for LOF variants in MODY genes is mainly based on case reports. C_LIO_LISystematic genetic evidence is needed to improve diagnosis and to inform gene-specific variant interpretation guidelines. C_LI What is the key question?O_LIDo NMD-triggering and NMD-escape LOF variants contribute to MODY across all known MODY genes? C_LI What are the new findings?O_LIHeterozygous NMD-escape LOF variants in INS are a novel cause of MODY. C_LIO_LIHeterozygous LOF variants in ABCC8 and KCNJ11 are not enriched in MODY. C_LIO_LIEnrichment of NMD-triggering and NMD-escape LOF variants differs across MODY genes, clarifying underlying mechanisms and supporting gene-specific interpretation. C_LI How might this impact on clinical practice in the foreseeable future?O_LIThese results improve the accuracy of MODY diagnosis by providing robust evidence for variant interpretation and supporting gene-specific clinical guidelines. C_LI