Co-segregation of the c.489+3A>G variant with p.Cys1400Ter pathogenic CFTR mutation in Cyprus: prevalence and clinical implications.

Background: The high variety of mutations found in the Cystic Fibrosis Transmembrane Regulator (CFTR) gene is responsible for the clinical heterogeneity observed in people with Cystic Fibrosis (CF) and the atypical manifestations in CFTR-related disorders (CFTR-RD). The intronic c.489+3A>G (c.621+3A>G) variant has been reported to have questionable pathogenicity, although its alleged severity was probably due to its co-segregation in cis with another undetected mutation, as previously reported from countries in the Mediterranean region. In the island of Cyprus, several rare CFTR variants have been previously identified, among them the c.489+3A>G in co-segregation with the pathogenic p.Cys1400Ter (cDNA name = c.4200_4201del or legacy name = 4332delTG) mutation. We aimed to investigate the prevalence of these variants in Cyprus and describe their clinical impact in patients and carriers.

Results: The intronic variant c.489+3A>G has been so far identified to co-segregate with the pathogenic p.Cys1400Ter mutation in the same allele in six unrelated Cypriot families and in total of 20 subjects. Three of them were diagnosed with CF, presenting with persistent respiratory symptoms, pancreatic insufficiency and a second CF-causing mutation. Two were diagnosed with CFTR-RD, presenting with bronchiectasis, intermediate sweat test and a second mutation known to cause CFTR-RD. Also, four carriers had a high suspicion of CFTR-RD, with bronchiectasis or emphysema and intermediate sweat test, although due to the lack of another CFTR mutation and a second functional test, definite diagnosis has not been made. Haplotype analysis provided evidence of a common haplotype in all individuals with co-segregation of the c.489+3A>G variant with p.Cys1400Ter mutation.

Conclusion: The intronic c.489+3A>G variant co-segregates extensively with p.Cys1400Ter in Cyprus as an ancestral combination due to a possible founder effect. Before providing genetic counselling to subjects identified through population screening to harbour the c.489+3A>G variant, extensive analysis of CFTR including gene rearrangements should be performed to identify possible other mutations in cis, especially in Mediterranean countries where this complex allele is probably common. Further research is warranted to fully delineate the clinical implications of the in cis co-segregation of p.Cys1400Ter with c.489+3A>G, even in the absence of pathogenic variants in the other CFTR allele.