Unsupervised Clustering of Missense Variants in HNF1A Using Multidimensional Functional Data Aids Clinical Interpretation

Abstract

Summary Exome sequencing in diabetes presents a diagnostic challenge because depending on frequency, functional impact, and genomic and environmental contexts, HNF1A variants can cause maturity-onset diabetes of the young (MODY), increase type 2 diabetes risk, or be benign. A correct diagnosis matters as it informs on treatment, progression, and family risk. We describe a multi-dimensional functional dataset of 73 HNF1A missense variants identified in exomes of 12,940 individuals. Our aim was to develop an analytical framework for stratifying variants along the HNF1A phenotypic continuum to facilitate diagnostic interpretation. HNF1A variant function was determined by four different molecular assays. Structure of the multi-dimensional dataset was explored using principal component analysis, k-means, and hierarchical clustering. Weights for tissue-specific isoform expression and functional domain were integrated. Functionally annotated variant subgroups were used to re-evaluate genetic diagnoses in national MODY diagnostic registries. HNF1A variants demonstrated a range of behaviors across the assays. The structure of the multi-parametric data was shaped primarily by transactivation. Using unsupervised learning methods, we obtained high-resolution functional clusters of the variants that separated known causal MODY variants from benign and type 2 diabetes risk variants and led to reclassification of 4% and 9% of HNF1A variants identified in the UK and Norway MODY diagnostic registries, respectively. Our proof-of-principle analyses facilitated informative stratification of HNF1A variants along the continuum, allowing improved evaluation of clinical significance, management, and precision medicine in diabetes clinics. Transcriptional activity appears a superior readout supporting pursuit of transactivation-centric experimental designs for high-throughput functional screens.

Maturity Onset Diabetes of the Young—New Approaches for Disease Modelling

“…Recently, an evaluation of different HNF1A mutations and their effects on clinical parameters were made. The results showed that the best and superior readout that correlated to clinical phenotype was for the transcriptional activity of the gene, therefore it was suggested that new high-throughput functional screens should be developed [ 53 ]. Interestingly, a homozygous missense HNF1A (pA251T) variant related to MODY was described recently [ 32 ].…”

100 YEARS OF INSULIN: A brief history of diabetes genetics: insights for pancreatic beta-cell development and function

“…More recently, our appreciation for the role of HNF1A in MODY has been expanded, as homozygous hypomorphic variants have also been identified as a cause of MODY (Misra et al 2020). These observations fit with a growing body of evidence demonstrating that genetic variation across the functional severity spectrum corresponds to phenotype (Althari et al 2020).…”

“…Functional studies have demonstrated that proteintruncating mutations result in haploinsufficiency (Harries et al 2004), whilst missense variants lead to loss of function through a variety of mechanisms (Althari et al 2020). More recently, our appreciation for the role of HNF1A in MODY has been expanded, as homozygous hypomorphic variants have also been identified as a cause of MODY (Misra et al 2020).…”

“…HNF4A) (Kathiresan et al 2009). These findings bring into focus a continuum between normal function and complete loss of function in these genesan allelic spectrum -where the relationship between the specific variant and subsequent disease presentation is not necessarily straightforward (Althari et al 2020). The genetic characterization of large Biobanks (e.g.…”

Molecular mechanisms of β-cell dysfunction and death in monogenic forms of diabetes

“…While some of them are associated with MODY3, e.g. the P291fsinsC mutation in exon 4 that is the most common Colclough, 2006, Colclough et al, 2013), others confer susceptibility for developing T2D, or are benign and neutral (Althari et al, 2020). MODY3 has high penetrance and is a very variable disease, even in siblings presenting severe insulin secretion defects.…”