Computational methods that allow predicting the effects of nonsynonymous substitutions are an integral part of exome studies. Here, we validated and improved their specificity by performing a comprehensive bioinformatics analysis combined with experimental and clinical data on a model of glucokinase (GCK): 8835 putative variations, including 515 disease-associated variations from 1596 families with diagnoses of monogenic diabetes (GCK-MODY) or persistent hyperinsulinemic hypoglycemia of infancy (PHHI), and 126 variations with available or newly reported (19 variations) data on enzyme kinetics. We also proved that high frequency of disease-associated variations found in patients is closely related to their evolutionary conservation. The default set prediction methods predicted correctly the effects of only a part of the GCK-MODY-associated variations and completely failed to predict the normoglycemic or PHHI-associated variations. Therefore, we calculated evidence-based thresholds that improved significantly the specificity of predictions (≤75%). The combined prediction analysis even allowed to distinguish activating from inactivating variations and identified a group of putatively highly pathogenic variations (EVmutation score <-7.5 and SNAP2 score >70), which were surprisingly underrepresented among MODY patients and thus under negative selection during molecular evolution. We suggested and validated the first robust evidence-based thresholds, which allow improved, highly specific predictions of disease-associated GCK variations.

Charles University 3rd Faculty of Medicine Prague Czech Republic

Zobrazit více v PubMed

Jetton TL, et al. Analysis of upstream glucokinase promoter activity in transgenic mice and identification of glucokinase in rare neuroendocrine cells in the brain and gut. J. Biol. Chem. 1994;269:3641–3654. PubMed

Lenzen S. A fresh view of glycolysis and glucokinase regulation: history and current status. J. Biol. Chem. 2014;289:12189–12194. doi: 10.1074/jbc.R114.557314. PubMed DOI PMC

Larion M, et al. Kinetic cooperativity in human pancreatic glucokinase originates from millisecond dynamics of the small domain. Angew. Chem. Int. Ed. 2015;127:8247–8250. doi: 10.1002/ange.201501204. PubMed DOI PMC

Osbak KK, et al. Update on mutations in glucokinase (GCK), which cause maturity‐onset diabetes of the young, permanent neonatal diabetes, and hyperinsulinemic hypoglycemia. Hum. Mutat. 2009;30:1512–1526. doi: 10.1002/humu.21110. PubMed DOI

George DC, et al. Evolution-and structure-based computational strategy reveals the impact of deleterious missense mutations on MODY 2 (maturity-onset diabetes of the young, type 2) Theranostics. 2014;4:366–385. doi: 10.7150/thno.7473. PubMed DOI PMC

Glaser B, et al. Familiar hyperinsulinism caused by an activating glucokinase mutation. N. Engl. J. Med. 1998;338:226–230. doi: 10.1056/NEJM199801223380404. PubMed DOI

Massa O, et al. High prevalence of glucokinase mutations in Italian children with MODY. Influence on glucose tolerance, first-phase insulin response, insulin sensitivity and BMI. Diabetologia. 2001;44:898–905. doi: 10.1007/s001250100530. PubMed DOI

Gloyn AL, et al. Prevalence of GCK mutations in individuals screened for fasting hyperglycaemia. Diabetologia. 2009;52:172–174. doi: 10.1007/s00125-008-1188-4. PubMed DOI

García-Herrero C-M, et al. Functional characterization of MODY2 mutations highlights the importance of the fine-tuning of glucokinase and its role in glucose sensing. PLoS ONE. 2012;7 doi: 10.1371/journal.pone.0030518. PubMed DOI PMC

Steele AM, et al. The previously reported T342P GCK missense variant is not a pathogenic mutation causing MODY. Diabetologia. 2011;54:2202–2205. doi: 10.1007/s00125-011-2194-5. PubMed DOI

Hopf TA, et al. Mutation effects predicted from sequence co-variation. Nat. Biotechnol. 2017;35:128–135. doi: 10.1038/nbt.3769. PubMed DOI PMC

Kamata K, Mitsuya M, Nishimura T, Eiki J, Nagata Y. Structural basis for allosteric regulation of the monomeric allosteric enzyme human glucokinase. Structure. 2004;12:429–438. doi: 10.1016/j.str.2004.02.005. PubMed DOI

Molnes J, et al. Binding of ATP at the active site of human pancreatic glucokinase-nucleotide-induced conformational changes with possible implications for its kinetic cooperativity. FEBS J. 2011;278:2372–2386. doi: 10.1111/j.1742-4658.2011.08160.x. PubMed DOI PMC

Ensembl genome browser 88. Available from http://www.ensembl.org/ (2017).

Flannick J, et al. Assessing the phenotypic effects in the general population of rare variants in genes for a dominant Mendelian form of diabetes. Nat. Genet. 2013;45:1380–1385. doi: 10.1038/ng.2794. PubMed DOI PMC

Dupuis J, et al. New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk. Nat. Genet. 2010;42:105–116. doi: 10.1038/ng.520. PubMed DOI PMC

Romeo S, et al. Rare loss-of-function mutations in ANGPTL family members contribute to plasma triglyceride levels in humans. J. Clin. Invest. 2009;119:70–79. PubMed PMC

Flanagan SE, Patch AM, Ellard S. Using SIFT and PolyPhen to predict loss-of-function and gain-of-function mutations. Genet. Test. Mol.Biomarkers. 2010;14:533–537. doi: 10.1089/gtmb.2010.0036. PubMed DOI

Rees MG, et al. Correlation of rare coding variants in the gene encoding human glucokinase regulatory protein with phenotypic, cellular, and kinetic outcomes. J. Clin. Invest. 2012;122:205–217. doi: 10.1172/JCI46425. PubMed DOI PMC

Johansen CT, Wang J, Lanktree MB. Excess of rare variants in genes identified by genome-wide association study of hypertriglyceridemia. Nat. Genet. 2010;42:684–687. doi: 10.1038/ng.628. PubMed DOI PMC

Beer NL, et al. Insights into the pathogenicity of rare missense GCK variants from the identification and functional characterization of compound heterozygous and double mutations inherited in cis. Diabetes Care. 2012;35:1482–1484. doi: 10.2337/dc11-2420. PubMed DOI PMC

Kanthimathi S, et al. Glucokinase gene mutations (MODY 2) in Asian Indians. Diabetes Technol. Therap. 2014;16:180–185. doi: 10.1089/dia.2013.0244. PubMed DOI

Estalella I, et al. Mutations in GCK and HNF-1α explain the majority of cases with clinical diagnosis of MODY in Spain. Clin. Endocrinol. 2007;67:538–546. PubMed

Valentínová L, et al. Identification and functional characterization of novel glucokinase mutations causing maturity-onset diabetes of the young in Slovakia. PLoS ONE. 2012;7 doi: 10.1371/journal.pone.0034541. PubMed DOI PMC

Sagen JV, et al. From clinicogenetic studies of maturity-onset diabetes of the young to unraveling complex mechanisms of glucokinase regulation. Diabetes. 2006;55:1713–1722. doi: 10.2337/db05-1513. PubMed DOI

Gloyn AL, et al. Insights into the structure and regulation of glucokinase from a novel mutation (V62M), which causes maturity-onset diabetes of the young. J. Biol. Chem. 2005;280:14105–14113. doi: 10.1074/jbc.M413146200. PubMed DOI

Rizzo MA, Piston DW. Regulation of β cell glucokinase by S-nitrosylation and association with nitric oxide synthase. J. Cell Biol. 2003;161:243–248. doi: 10.1083/jcb.200301063. PubMed DOI PMC

Pruhova S, et al. Glucokinase diabetes in 103 families from a country-based study in the Czech Republic: geographically restricted distribution of two prevalent GCK mutations. Pediatr. Diabetes. 2010;11:529–535. doi: 10.1111/j.1399-5448.2010.00646.x. PubMed DOI

Milenković T, Zdravković D, Mitrović K. [Novel glucokinase mutation in a boy with maturity-onset diabetes of the young] Srp. Arh. Celok. Lek. 2008;136:542–544. doi: 10.2298/SARH0810542M. PubMed DOI

Pinterova D, et al. Six novel mutations in the GCK gene in MODY patients. Clin. Genet. 2007;71:95–96. doi: 10.1111/j.1399-0004.2006.00729.x. PubMed DOI

Cárdenas ML, Rabajille E, Niemeyer H. Suppression of kinetic cooperativity of hexokinase D (glucokinase) by competitive inhibitors. A slow transition model. Eur. J. Biochem. 1984;145:163–171. doi: 10.1111/j.1432-1033.1984.tb08536.x. PubMed DOI

Wolf AJ, et al. Hexokinase is an innate immune receptor for the detection of bacterial peptidoglycan. Cell. 2016;166:624–636. doi: 10.1016/j.cell.2016.05.076. PubMed DOI PMC

Lukášová P, et al. Screening of mutations and polymorphisms in the glucokinase gene in Czech diabetic and healthy control populations. Physiol. Res. 2008;57:S99–S108. PubMed

Pruhova S, et al. Genetic epidemiology of MODY in the Czech republic: new mutations in the MODY genes HNF-4α, GCK and HNF-1α. Diabetologia. 2003;46:291–295. doi: 10.1007/s00125-002-1010-7. PubMed DOI

Urbanová J, et al. Positivity for islet cell autoantibodies in patients with monogenic diabetes is associated with later diabetes onset and higher HbA1c level. Diabet. Med. 2014;31:466–471. doi: 10.1111/dme.12314. PubMed DOI

García-Herrero CM, et al. Functional analysis of human glucokinase gene mutations causing MODY2: exploring the regulatory mechanisms of glucokinase activity. Diabetologia. 2007;50:325–333. doi: 10.1007/s00125-006-0542-7. PubMed DOI

Davis EA, et al. Mutants of glucokinase cause hypoglycaemia- and hyperglycaemia syndromes and their analysis illuminates fundamental quantitative concepts of glucose homeostasis. Diabetologia. 1999;42:1175–1186. doi: 10.1007/s001250051289. PubMed DOI

Matschinsky FM. Assessing the potential of glucokinase activators in diabetes therapy. Nat. Rev. Drug Discov. 2009;8:399–416. doi: 10.1038/nrd2850. PubMed DOI

Matschinsky, F. M. et al. The glucokinase system and the regulation of blood sugar. In Matschinsky, D. M. & Magnuson, M. A., Eds Molecular pathogenesis of MODYs. Basel, Karger, pp. 99–108 (2000).

Refinement of evolutionary medicine predictions based on clinical evidence for the manifestations of Mendelian diseases

Identification of alkaline pH optimum of human glucokinase because of ATP-mediated bias correction in outcomes of enzyme assays