ClinVar Genomic variation as it relates to human health

This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 349 of the CFTR protein (p.Ala349Val). This variant is present in population databases (rs121909021, gnomAD 0.02%). This missense change has been observed in individuals with CFTR-related diseases, including recurrent pancreatitis, cystic fibrosis (CF), CF-related metabolic syndrome, and congenital bilateral absence of the vas deferens (PMID: 15070876, 15638824, 17003641, 22094894, 25754095, 26671754). ClinVar contains an entry for this variant (Variation ID: 7172). 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: 30046002). 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.

The CFTR c.1046C>T; p.Ala349Val variant has been reported in patients diagnosed with congenital bilateral absence of vas deferens (Dayangac 2004) or pancreatitis (Keiles 2006), when found in-trans with pathogenic CFTR variants (Dayangac 2004). Functional studies show this variant to have approximately 45% of wild type function (Raraigh 2018). The observed variant has been submitted to ClinVar with conflicting interpretation of pathogenicity (Pathogenic/Likely Pathogenic/ Variant of Uncertain Significance). The p.Ala349Val variant is reported with the allele frequency (0.01%) in the gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. The amino acid Ala at position 349 is changed to a Val changing protein sequence and it might alter its composition and physico-chemical properties. The variant is predicted to be damaging by PolyPhen2 and the residue is conserved across species. The amino acid change p.Ala349Val in CFTR is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. According to Cystic fibrosis mutation database, the effect of homozygous mutation on this disorder is uncertain, hence the variant has been classified as a Variant of Uncertain Significance (VUS).

This variant has been reported in the published literature in individuals with pancreatic sufficient cystic fibrosis (PMID: 25754095 (2015)), pancreatitis (PMID: 17003641 (2006), 22094894 (2012)), congenital bilateral absence of the vas deferens (CBAVD) (PMID: 8627844 (1996), 15070876 (2004)), and CFTR-related metabolic syndrome (CRMS) (PMID: 26671754 (2016)). A functional assay found this variant showed decreased CFTR function compared to wild-type (PMID: 29805046 (2018)). The frequency of this variant in the general population, 0.00022 (28/128882 chromosomes (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 deleterious or benign. Based on the available information, we are unable to determine the clinical significance of this variant.

The CFTR c.1046C>T; p.Ala349Val variant (rs121909021) has been reported in patients diagnosed with congenital bilateral absence of vas deferens (Dayangac 2004, Havasi 2010) or pancreatitis (Keiles 2006, Sultan 2010), when found in-trans with pathogenic CFTR variants (Dayangac 2004, Sultan 2012). Functional studies show this variant to have approximately 45% of wild type function (Raraigh 2018). This variant is reported in ClinVar (Variation ID: 7172). It is found in the general population with an overall allele frequency of 0.01% (32/282468 alleles) in the Genome Aggregation Database. Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.632). Due to its reported occurrence in CFTR-related disorders, the p.Ala349Val variant is classified as mildly pathogenic. References: Dayangac D et al. Mutations of the CFTR gene in Turkish patients with congenital bilateral absence of the vas deferens. Hum Reprod. 2004 May;19(5):1094-100. PMID: 15070876. Havasi V et al. Association of cystic fibrosis genetic modifiers with congenital bilateral absence of the vas deferens. Fertil Steril. 2010 Nov;94(6):2122-7. PMID: 20100616. Keiles S et al. Identification of CFTR, PRSS1, and SPINK1 mutations in 381 patients with pancreatitis. Pancreas. 2006 Oct;33(3):221-7. PMID: 17003641. Sultan M et al. Genetic prevalence and characteristics in children with recurrent pancreatitis. J Pediatr Gastroenterol Nutr. 2012 May;54(5):645-50. PMID: 22094894. 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.

Variant summary: CFTR c.1046C>T (p.Ala349Val) results in a non-conservative amino acid change located in the ABC transporter transmembrane region 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 0.00011 in 251726 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in CFTR causing Non-Classic Cystic Fibrosis (0.00011 vs 0.013), allowing no conclusion about variant significance. c.1046C>T has been reported in the literature as a non-informative genotype in individuals ranging from a healthy carrier male, CBAVD, laboratory based CF genotyping cohorts, pancreatitis, pancreatically sufficient CF and cystic fibrosis transmembrane regulator-related metabolic syndrome with normal sweat chloride levels (example, Audrezet_1993, Schlegel_1996, Scotet_2001, Ravnik-Glavac_2002, Castaldo_2005, Lucarelli_2006, Sultan_2012, Wooldridge_2015, Schwartz_2009, Havasi_2010, Keiles_2006, Levy_2016, Tamura_2018, McCague_2019). In our conservative assessment, these data do not allow any conclusion about variant significance. Two publications reporting experimental evidence evaluating an impact on protein function were ascertained in the context of this evaluation. The most pronounced variant effect results in 30%-50% of normal CFTR activity with a categorization as indeterminate (Raraigh_2018, Han_2018). The following publications have been ascertained in the context of this evaluation (PMID: 11168024, 17003641, 15638824, 19324992, 11933191, 7683952, 16635477, 8627844, 22094894, 20100616, 25735457, 25754095, 29805046, 30046002, 29669919, 26671754, 30888834). ClinVar contains an entry for this variant (Variation ID: 7172). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.

CFTR variant of uncertain clinical significance. See www.CFTR2.org for phenotype information.

The p.A349V variant (also known as c.1046C>T), located in coding exon 8 of the CFTR gene, results from a C to T substitution at nucleotide position 1046. The alanine at codon 349 is replaced by valine, an amino acid with similar properties. This variant was identified in one individual with congenital bilateral absence of the vas deferens (CBAVD) and one individual with recurrent acute pancreatitis; both individuals were also heterozygous for a pathogenic mutation, but the phase is unknown (Dayangaç D et al. Hum. Reprod., 2004 May;19:1094-100; Sultan M et al. J. Pediatr. Gastroenterol. Nutr., 2012 May;54:645-50). In CFBE cells, this variant demonstrated 45% of wild type CFTR function (Raraigh KS et al. Am. J. Hum. Genet., 2018 Jun;102:1062-1077). This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on available evidence to date, the clinical significance of this alteration remains unclear.

In silico analysis indicates that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 34405919, 8627844, 11933191, 16635477, 15024729, 19324992, 25304080, 25735457, 33500538, 30046002, 7683952, 17003641, 31036917, 25087612, 26671754, 23523379, 25754095, 11168024, 15070876, 15638824, 20100616, 22094894, 29669919, 30888834, 33922413, 19897426, 34996830, 35652053, 36253274, 37873426, 29805046)