The number of complex cystic fibrosis transmembrane conductance regulator (CFTR) genotypes identified as having double-mutant alleles with two mutations inherited in cis has been growing. We investigated the structure-function relationships of a severe cystic fibrosis (CF)-associated double mutant (R347H-D979A) to evaluate the contribution of each mild mutation to the phenotype. CFTR mutants expressed in HeLa cells were analyzed for protein biosynthesis and Cl ؊ channel activity. Our data show that R347H is associated with mild defective Cl ؊ channel activity and that the D979A defect leads to misprocessing. The mutant R347H-D979A combines both defects for a dramatic decrease in Cl ؊ current. To decipher the molecular mechanism of this phenotype, single and double mutants with different charge combinations at residues 347 and 979 were constructed as charged residues were involved in this complex genotype. These studies revealed that residue 979, located in the third cytoplasmic loop, is critical for CFTR processing and Cl ؊ channel activity highlighting the role of charged residues. These results have also important implications for CF, as they show that two mutations in cis can act in concert to alter dramatically CFTR function contributing to the wide phenotypic variability of CF disease.The cystic fibrosis transmembrane conductance regulator (CFTR) 1 protein is a cAMP-regulated chloride channel located in the apical membrane of epithelial cells. CFTR is predicted to consist of twelve putative membrane-spanning segments (TM), two nucleotide-binding domains, a regulatory domain, and four cytoplasmic loops (CL) connecting the TMs on the cytoplasmic side of the protein (1). Mutations in the CFTR gene cause cystic fibrosis (CF), the most common genetic disease in Caucasians.The number of complex CFTR genotypes identified, including double-mutant alleles where two missense mutations are carried by the same chromosome, has been growing (2-6). It is difficult to evaluate the contribution of each mutation/or polymorphism to the phenotype as mutations in cis may act in concert to alter or reverse defective CFTR function and thus modify the CF phenotype (2).The recent discovery of severe CF associated with a ⌬F508/ R347H-D979A compound heterozygote genotype in two related patients suffering from pancreatic insufficiency and severe respiratory symptoms suggests that the R347H-D979A mutation has an important influence on CFTR processing and/or function (7). At least four CF-associated mutations have been identified in isolation at position 347 (R347C, R347H, R347L, and R347P) and two at position 979 (D979A and D979V), suggesting that Arg-347 and Asp-979 are important for CFTR structure and/or function. The mutation D979A was found in isolation in a patient with a congenital bilateral absence of the vas deferens (8) and the R347H mutation in CF patients with pancreatic sufficiency, congenital bilateral absence of the vas deferens, and no or mild pulmonary symptoms (7). As the R347H mutation is mostly associated with mild C...