PharmGKB Level of Evidence 1A: Level 1A clinical annotations describe variant-drug combinations that have variant-specific prescribing guidance available in a current clinical guideline annotation or an FDA-approved drug label annotation. Annotations of drug labels or clinical guidelines must give prescribing guidance for specific variants (e.g. CYP2C9*3, HLA-B*57:01) or provide mapping from defined allele functions to diplotypes and phenotypes to be used as supporting evidence for a level 1A clinical annotation. Level 1A clinical annotations must also be supported by at least one publication in addition to a clinical guideline or drug label with variant-specific prescribing guidance.

Variant summary: CFTR c.1055G>A (p.Arg352Gln) results in a conservative amino acid change in 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 2.4e-05 in 251124 control chromosomes (gnomAD). c.1055G>A has been reported in the literature in multiple individuals affected with Cystic Fibrosis (e.g. Dupuis_2015, Shackelton_1994, Sosnay_2013). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function, and demonstrated that the variant leads to defective chloride channel function (Sosnay 2013). Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, and all of them classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

The CFTR c.1055G>A; p.Arg352Gln variant (rs121908753) is reported in the literature in several individuals affected with cystic fibrosis (Masson 2013, Ooi 2012, Sosnay 2013). This variant is also reported in ClinVar (Variation ID: 7198), and is only observed on six alleles in the Genome Aggregation Database, indicating it is not a common polymorphism. The arginine at codon 352 is highly conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.804). Additionally, functional assays demonstrate reduced protein function (Van Goor 2014). Based on available information, this variant is considered to be pathogenic. References Masson E et al. A conservative assessment of the major genetic causes of idiopathic chronic pancreatitis: data from a comprehensive analysis of PRSS1, SPINK1, CTRC and CFTR genes in 253 young French patients. PLoS One. 2013 Aug 8;8(8):e73522. PMID: 23951356. Ooi CY et al. Cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations in pancreatitis. J Cyst Fibros. 2012 Sep;11(5):355-62. PMID: 22658665. 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. Van Goor F et al. Effect of ivacaftor on CFTR forms with missense mutations associated with defects in protein processing or function. J Cyst Fibros. 2014 Jan;13(1):29-36. PMID: 23891399.

NM_000492.4(CFTR):c.1055G>A (p.Arg352Gln) is a missense variant that results in the substitution of arginine with glutamine. Functional evidence supports a deleterious effect on the gene or gene product (PMID: 23709221; PMID: 7544319; PMID: 27086061; PMID: 28646244; PMID: 18456578). This variant has been recurrently observed in individuals with related phenotype (PMID: 23709221; PMID: 7544319; PMID: 27086061; PMID: 28646244; PMID: 18456578). Multiple computational predictions support a deleterious effect on the gene or gene product. The variant is present at low frequency in population datasets. Based on the available data, this variant is classified as pathogenic.

NM_000492.3(CFTR):c.1055G>A(R352Q) is classified as pathogenic in the context of cystic fibrosis and is associated with the non-classic form of disease. Sources cited for classification include the following: PMID 18456578 and 23974870. Classification of NM_000492.3(CFTR):c.1055G>A(R352Q) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.‚Äã

Previously reported disease-causing CFTR variant. See www.CFTR2.org for phenotype information.

PS3, PM3_Supporting, PP3, PM1, PM2

The variant was found in a symptomatic patient. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. The variant occurs with multiple lone recessive pathogenic variants in the same gene. Functional studies have shown that this variant has a deleterious effect on protein function.

The p.R352Q pathogenic mutation (also known as c.1055G>A), located in coding exon 8 of the CFTR gene, results from a G to A substitution at nucleotide position 1055. The arginine at codon 352 is replaced by glutamine, an amino acid with highly similar properties. This mutation was first reported in an individual with pancreatic sufficient cystic fibrosis (CF) and an unknown variant on the other chromosome (Cremonesi L et al. Hum. Mutat., 1992;1:314-9). In two additional studies, p.R352Q was reported in conjunction with p.F508del in an individual with CF and an individual with idiopathic chronic pancreatitis (Zitkiewicz E et al. PLoS ONE, 2014 Mar;9:e89094; Steiner B et al. Hum. Mutat., 2011 Aug;32:912-20). This mutation is associated with pancreatic sufficiency and elevated sweat chloride levels (Sosnay PR et al. Nat. Genet., 2013 Oct;45:1160-7). In a functional study using a Xenopus laevis oocyte model, alterations affecting the positive charge at codon 352 (p.R352A, p.R352E, p.R352Q) were observed to alter pore structure by disrupting the interaction between R352 and D993 (Cui G et al. J. Membr. Biol., 2008 Mar;222:91-106). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

The observed missense variant c.1055G>A (p.Arg352Gln) in the CFTR gene has been reported in homozygous and compound heterozygous state in individuals affected with cystic fibrosis (Nowak JK, et al., 2017, Sosnay PR, et al., 2013). Experimental evidence suggests this variant results in reduced protein function (Van Goor F, et al., 2014). This p.Arg352Gln variant has 0.002% allele frequency in the gnomAD. This variant has been submitted to the ClinVar database as drug response/Pathogenic (multiple submissions). The reference amino acid p.Arg352Gln in CFTR is predicted as conserved by GERP++ and PhyloP across 100 vertebrates.Multiple lines of computational evidence (Polyphen-probably damaging, SIFT-damaging and Mutation Taster-disease causing) predict a damaging effect on protein structure and function for this variant The amino acid Arginine at position 352 is changed to a Glutamine changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic.

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 352 of the CFTR protein (p.Arg352Gln). This variant is present in population databases (rs121908753, gnomAD 0.01%). This missense change has been observed in individual(s) with cystic fibrosis (PMID: 7544319, 20522854, 27086061, 28646244). ClinVar contains an entry for this variant (Variation ID: 7198). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt CFTR protein function with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.

The c.1055G>A variant in CFTR is a missense variant predicted to cause substitution of arginine to glutamine at amino acid 352. This variant is rare in the general population with a frequency below the threshold expected for the associated phenotype(s). This variant has been observed in one or more individuals affected with the associated recessive disease, as either homozygous or compound heterozygous with a second variant (PMID: 26087176). Computational prediction algorithms indicate this variant is likely to affect gene or protein function. Given the available evidence, this variant is classified as Pathogenic.

PS3: Well-established in vitro and in vivo functional studies supportive of damaging effect on the gene product, with low residual enzymatic activity relative to wild-type reported (PMID: 23891399, 23974870); PM2: Maximum gnomAD MAF of 0.0044% in South Asian (SAS) subpopulation (<0.28% threshold); PM3_Strong: Variant reported in homozygous state in one affected individual and in trans with 4 pathogenic variants in 6 individuals affected with cystic fibrosis (PMID: 7544319, 19318346, 21520337, 27659740); PM5: Likely pathogenic missense amino acid change occurs in same position: c.1054C>T; p.Arg352Trp (PMID: 19897426); PP3: In-silico models predict deleterious effect (Revel = 0.8, BayesDel = 0.4)