ClinVar Genomic variation as it relates to human health

CFTR c.535C>A has been identified in multiple individuals with elevated sweat chloride concentration and features of cystic fibrosis who also have a second CFTR variant, although the phase of these variants is not known. This variant (rs367850319) is rare (<0.1%) in a large population dataset (gnomAD: 4/250702 total alleles; 0.0016%; no homozygotes) and has been reported in ClinVar (Variation ID: 53993). BayPR, an algorithm that uses population data to assign disease liability to variants, predicts that this variant is unlikely to be CF-causing. A single in vitro functional study suggests that this variant is associated with a decrease in CFTR function, but this decrease is not to the level observed with other CF-causing variants in this study. This functional data has not been replicated to our knowledge. The glutamine at this position is evolutionarily conserved across all species assessed. Due to insufficient evidence that this variant is deleterious, we consider the clinical significance of CFTR c.535C>A to be uncertain at this time.

The p.Q179K variant (also known as c.535C>A), located in coding exon 5 of the CFTR gene, results from a C to A substitution at nucleotide position 535. The glutamine at codon 179 is replaced by lysine, an amino acid with similar properties. This variant was observed with another pathogenic CFTR alteration in a Hispanic patient who had elevated sweat chloride level, pulmonary symptoms, and pancreatic insufficiency (Wong LJ et al. Hum. Mutat., 2001 Oct;18:296-307). In vitro studies have demonstrated that the variant results in reduced CFTR maturation and function (Caputo A et al. J. Pharmacol. Exp. Ther., 2009 Sep;330:783-91; Okiyoneda T et al. Nat Chem Biol, 2013 Jul;9:444-54). However, it remains unknown if the observed reduction is sufficient to cause disease. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

The CFTR c.535C>A; p.Gln179Lys variant (rs367850319) is reported in the literature in individuals affected with cystic fibrosis (CF) or CFTR-related disorders, however, a second variant was not identified in these individuals (Casals 2004, Keiles 2006, Schrijver 2005, Wong 2004). One individual with CF was reported to carry a second pathogenic CFTR variant, but the phase of the two variants was not determined (Wong 2001). This variant is reported in ClinVar (Variation ID: 53993), and is only observed on four alleles in the Genome Aggregation Database, indicating it is not a common polymorphism. The glutamine at codon 179 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. In vitro functional analyses demonstrate a maturation defect but partial protein function (Caputo 2009). Due to limited information, the clinical significance of this variant is uncertain at this time. REFERENCES Caputo A et al. Mutation-specific potency and efficacy of cystic fibrosis transmembrane conductance regulator chloride channel potentiators. J Pharmacol Exp Ther. 2009 Sep;330(3):783-91. Casals T et al. Bronchiectasis in adult patients: an expression of heterozygosity for CFTR gene mutations? Clin Genet. 2004 Jun;65(6):490-5. Keiles S and Kammesheidt A. Identification of CFTR, PRSS1, and SPINK1 mutations in 381 patients with pancreatitis. Pancreas. 2006 Oct;33(3):221-7. Schrijver I et al. Diagnostic testing by CFTR gene mutation analysis in a large group of Hispanics: novel mutations and assessment of a population-specific mutation spectrum. J Mol Diagn. 2005 May;7(2):289-99. Wong LJ et al. Improved detection of CFTR mutations in Southern California Hispanic CF patients. Hum Mutat. 2001 Oct;18(4):296-307. Wong LJ and Alper OM. Detection of CFTR mutations using temporal temperature gradient gel electrophoresis. Electrophoresis. 2004 Aug;25(15):2593-601.

Reported previously with a second variant in a patient with cystic fibrosis including pancreatic insufficiency (Wong et al., 2001); Also reported as heterozygous with no second variant identified in patients with pancreatitis or bronchiectasis (Giefer et al., 2017; Casals et al., 2004); Although published functional studies showed reduced maturation, iodide transport measured in COS-7 cells were inconsistent with this variant being a CF-causing mutation (Caputo et al., 2009); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 18556774, 16049310, 15151509, 28502372, 11668613, 15300780, 19491324, 25087612, 15858154)

This sequence change replaces glutamine, which is neutral and polar, with lysine, which is basic and polar, at codon 179 of the CFTR protein (p.Gln179Lys). This variant is present in population databases (rs367850319, gnomAD 0.002%). This missense change has been observed in individual(s) with clinical features of cystic fibrosis (PMID: 11668613). ClinVar contains an entry for this variant (Variation ID: 53993). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt CFTR protein function. Experimental studies have shown that this missense change affects CFTR function (PMID: 19491324, 23666117). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

Variant summary: CFTR c.535C>A (p.Gln179Lys) results in a conservative amino acid change located in the ABC transporter type 1, transmembrane domain (IPR011527) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.6e-05 in 250702 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.535C>A has been reported in the literature in patients with CF (n=2) as well as CFTR-related phenotypes such as pancreatitis (n=1) and bronchiectasis (n=1) without strong evidence for or against pathogenicity (e.g. Wong_2001, Casals_2004, Keiles_2006, Schrijver_2005). In one CF patient, it was reported in compound heterozygosity with another truncating variant; however, it is not specified whether such zygosity was confirmed by parental testing (Wong_2001/Sickkids db). It has also been reported in the compound heterozygous state together with F508del in an individual who was CF screen-positive with an inconclusive diagnosis as an infant, yet who did not receive a change in diagnosis during a follow-up period of approximately 7 years (Gonska_2021). These data do not allow any conclusion about variant significance. At least two publications report experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in a significantly reduced maturation and iodide transport measured in COS-7 cells at levels not consistent with that for a CF-causing mutation (Caputo_2009, Okiyoneda_2013). The following publications have been ascertained in the context of this evaluation (PMID: 34740355, 19491324, 15151509, 34814176, 17003641, 23666117, 16049310, 15858154, 18556774, 15300780, 11668613). Nine submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.