Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene

Allelic heterogeneity in disease-causing genes presents a substantial challenge to the translation of genomic variation into clinical practice. Few of the almost 2,000 variants in the cystic fibrosis transmembrane conductance regulator gene CFTR have empirical evidence that they cause cystic fibrosis. To address this gap, we collected both genotype and phenotype data for 39,696 individuals with cystic fibrosis in registries and clinics in North America and Europe. In these individuals, 159 CFTR variants had an allele frequency of ≥0.01%. These variants were evaluated for both clinical severity and functional consequence, with 127 (80%) meeting both clinical and functional criteria consistent with disease. Assessment of disease penetrance in 2,188 fathers of individuals with cystic fibrosis enabled assignment of 12 of the remaining 32 variants as neutral, whereas the other 20 variants remained of indeterminate effect. This study illustrates that sourcing data directly from well-phenotyped subjects can address the gap in our ability to interpret clinically relevant genomic variation.This work was supported by grants from the NIDDK (5R37DK044003 to G.R.C.) and the US NIH (DK49835 to P.J.T.) and by funding from Cystic Fibrosis Foundation Therapeutics, Inc. (to P.J.T.), the US Cystic Fibrosis Foundation (CUTTING08A, CUTTING09A and CUTTING10A to G.R.C. and SOSNAY10Q to P.R.S.) and FCTPortugal (PIC/IC/83103/2007 and PEstOE/BIA/UI4046/2011 to M.D.A. and BioFIG)