This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

CFTR: BS1

The R31C variant in the CFTR gene was first identified in the homozygous state in an asymptomatic individual and reported as a benign polymorphism (Ghanem et al., 1994). Other publications have reported this variant in association with disseminated bronchiectasis (Girodon et al., 1997), idiopathic pancreatitis (Gomez Lira et al., 2001), and oligospermia (Gallati et al., 2009), though a second CFTR variant was not identified in these cases. The R31C variant was not observed with any significant frequency in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The R31C variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position where amino acids with similar properties to Arginine are tolerated across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. A missense variant in the same residue (R31L) was identified in an adult woman with pulmonary symptoms but normal pulmonary function, normal pancreatic function, and repeated abnormal sweat chloride levels (mean value 90.9 mmol/L); no second CFTR variant was identified (Zielenski et al., 1995). Functional studies performed show that R31C affects protein biogenesis, although the defect is not complete (Jurkuvenaite et al., 2006). While the R31C variant has been deemed not to be cystic fibrosis-causing (Sosnay et al., 2013), it is possible this variant may have reduced penetrance in association with CF-related disorders. We interpret R31C as a variant of unknown significance.

Variant summary: c.91C>T affects a conserved nucleotide, resulting in amino acid change from Arg to Cys. 5/5 in-silico tools predict damaging outcome. This variant was found in 214/124456 control chromosomes at a frequency of 0.0017195, including 1 homozygous occurrence. This frequency does not significantly exceed maximal expected frequency of a pathogenic allele (0.0129603) for non-classic CF. This variant has been found in patients with atypical CF, ICP and asthma-like bronchopathy. Variant was also found in healthy individuals, including 1 compound heterozygote with F508del with no symptoms suggestive of CF, 1 homozygous asymptomatic 6 y.o. child with family member presented with asthma-like bronchopathy (Ghanem_1994) and one homozygote in ExAC database. CFTR2 database classified this variant as non-CF-casuing based on clinical and functional data (Sosnay_2013). A case-control study including more than 2000 samples showed odds ratio of this variant associated with pancreatitis was 0.42, suggesting this variant does not increase the risk to develop pancreatitis (LaRusch_2014). Taken together, this variant was classified as Benign.

This variant was classified based on the report of 1 patient with a clinically confirmed diagnosis of cystic fibrosis in the context of re-classifying variants in the German Cystic Fibrosis Registry (Muko e.V.). Patients have not been seen personally, but only reports were evaluated. Criteria applied:PP3, PM5_STR, BP6, BS3_SUP, BS2

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

The CFTR c.91C>T (p.Arg31Cys) variant has been reported in the published literature in affected individuals with mild cystic fibrosis (CF) (PMID: 9272738 (1997)), pancreatitis (PMIDs: 12120234 (2001), 25033378 (2014), 25383785 (2015), 25492507 (2015), 25869325 (2015), 28544683 (2017)), and bronchiectasis (PMIDs: 7522211 (1994), 28544683 (2017), 29997923 (2018)). The variant has also been observed in reportedly healthy individuals (PMIDs: 23514810 (2013), 25033378 (2014), 29997923 (2018)), including an individual in a homozygous state (PMID: 7522211 (1994)). The variant does not prevent chloride conduction by the CFTR protein in functional studies (PMID: 25824995 (2015)), but it has been reported as causing reduced CFTR protein activity by enhancing endocytosis of the CFTR protein (PMID: 16339147 (2006)). The frequency of this variant in the general population (Genome Aggregation Database, http://gnomad.broadinstitute.org) is uninformative in the assessment of its pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded conflicting predictions that this variant is benign or damaging. Based on the available information, we are unable to determine the clinical significance of this variant.

BP6, PP3

The CFTR c.91C>T; p.Arg31Cys variant (rs1800073) is reported in individuals with idiopathic pancreatitis (Bernardino 2000, Gomez-Lira 2001, Hirai 2023), oligospermia (Gallati 2009), bronchiectasis (Guan 2018, Lawless 2023), mild pulmonary disorders (Ghanem 1994), and congenital absence of the vas deferens (Fang 2022). Although initial functional studies suggested a defect in CFTR processing and chloride transport activity (Jurkuvenaite 2006), subsequent studies indicated no defects (Sosnay 2013). In addition, the variant has been reported as a homozygote in an asymptomatic individual (Ghanem 1994) and was shown not to be enriched in individuals diagnosed with pancreatitis (LaRusch 2014). This variant is reported in ClinVar (Variation ID: 35893), and found in the general population with an overall allele frequency of 0.2% (463/282,310 alleles, including 1 homozygote) in the Genome Aggregation Database (v2.1.1). Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.669). However, another variant at this codon (p.Arg31Leu) has been reported in an individual with elevated sweat chloride levels (Zielenski 1995) and exhibited 56% of wildtype chloride channel activity in functional assays (Raraigh 2018). Due to the conflicting information regarding this variant, its clinical significance is uncertain at this time. References: Bernardino AL et al. Molecular analysis in Brazilian cystic fibrosis patients reveals five novel mutations. Genet Test. 2000;4(1):69-74. PMID: 10794365 Fang J et al. Congenital absence of the vas deferens with hypospadias or without hypospadias: Phenotypic findings and genetic considerations. Front Genet. 2022 Nov 9;13:1035468. PMID: 36437957. Gallati S et al. Cystic fibrosis transmembrane conductance regulator mutations in azoospermic and oligospermic men and their partners. Reprod Biomed Online. 2009 Nov;19(5):685-94. PMID: 20021716 Ghanem N et al. Identification of eight mutations and three sequence variations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Genomics. 1994 May 15;21(2):434-6. PMID: 7522211 Gomez-Lira M et al. CFTR and cationic trypsinogen mutations in idiopathic pancreatitis and neonatal hypertrypsinemia. Pancreatology. 2001;1(5):538-42. PMID: 12120234 Guan WJ et al. Next-generation sequencing for identifying genetic mutations in adults with bronchiectasis. J Thorac Dis. 2018 May;10(5):2618-2630. PMID: 29997923 Hirai S et al. The Coexistence of TRPV6 Variants With Other Pancreatitis-Associated Genes Affects Pediatric-Onset Pancreatitis. J Pediatr Gastroenterol Nutr. 2023 Apr 1;76(4):483-488. PMID: 36599151. Jurkuvenaite A et al. Mutations in the amino terminus of the cystic fibrosis transmembrane conductance regulator enhance endocytosis. J Biol Chem. 2006 Feb 10;281(6):3329-34. PMID: 16339147 Lawless D et al. Prevalence of CFTR variants in primary immunodeficiency patients with bronchiectasis is an important modifying cofactor. J Allergy Clin Immunol. 2023 Jul;152(1):257-265. PMID: 36828084. LaRusch J et al. Mechanisms of CFTR functional variants that impair regulated bicarbonate permeation and increase risk for pancreatitis but not for cystic fibrosis. PLoS Genet. 2014 Jul 17;10(7):e1004376. PMID: 25033378 Raraigh KS et al. Functional Assays Are Essential for Interpretation of Missense Variants Associated with Variable Expressivity. Am J Hum Genet. 2018 Jun 7;102(6):1062-1077. PMID: 29805046 Sosnay PR et al. Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene. Nat Genet. 2013 Oct;45(10):1160-7. PMID: 23974870 Zielenski J et al. Identification of six mutations (R31L, 441delA, 681delC, 1461ins4, W1089R, E1104X) in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Hum Mutat. 1995;5(1):43-7. PMID: 7537150