ClinVar Genomic variation as it relates to human health

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.

The CFTR c.2173G>A; p.Glu725Lys variant (rs199791061) has been described in patients with cystic fibrosis, but without strong evidence for pathogenicity (des Georges 2004, Kanavakis 2003). This variant has also been reported in the heterozygous state in one individual with suboptimal fertility and one individual affected with hypertrypsinemia (Gene 2008, Larriba 2005). This variant is also reported in ClinVar (Variation ID: 53448). This variant is found in the general population with an overall allele frequency of 0.009% (28/282634 alleles) in the Genome Aggregation Database. The glutamic acid at codon 725 is moderately conserved, computational analyses predict that this variant is deleterious (REVEL: 0.77). However, given the lack of clinical and functional data, the significance of the p.Glu725Lys variant is uncertain at this time. References: Des Georges M et al. High heterogeneity of CFTR mutations and unexpected low incidence of cystic fibrosis in the Mediterranean France. J Cyst Fibros. 2004 Dec;3(4):265-72. Gene G et al. N-terminal CFTR missense variants severely affect the behavior of the CFTR chloride channel. Hum Mutat. 2008 May;29(5):738-49. Kanavakis E et al. Cystic fibrosis in Greece: molecular diagnosis, haplotypes, prenatal diagnosis and carrier identification amongst high-risk individuals. Clin Genet. 2003 May;63(5):400-9. Larriba S et al. Molecular evaluation of CFTR sequence variants in male infertility of testicular origin. Int J Androl. 2005 Oct;28(5):284-90.

This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 725 of the CFTR protein (p.Glu725Lys). This variant is present in population databases (rs199791061, gnomAD 0.02%). This missense change has been observed in individual(s) with cystic fibrosis (PMID: 12752573, 15698946, 18306312). ClinVar contains an entry for this variant (Variation ID: 53448). 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. 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 p.E725K variant (also known as c.2173G>A), located in coding exon 14 of the CFTR gene, results from a G to A substitution at nucleotide position 2173. The glutamic acid at codon 725 is replaced by lysine, an amino acid with similar properties. This variant has been detected in individuals with cystic fibrosis (des Georges M et al. J. Cyst. Fibros., 2004 Dec;3:265-72, Claustres M et al. Hum Mutat, 2017 10;38:1297-1315, Kanavakis E et al. Clin Genet, 2003 May;63:400-9). In addition, the alteration has been reported in patients with idiopathic chronic pancreatitis, primary sclerosing cholangitis, suboptimal fertility, and hypertrypsinemia (Zou WB et al. Clin Transl Gastroenterol, 2018 11;9:204, Pall H et al. J Pediatr, 2007 Sep;151:255-9, Larriba S et al. Int J Androl, 2005 Oct;28:284-90, Gené GG et al. Hum Mutat, 2008 May;29:738-49).). 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. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

Variant summary: CFTR c.2173G>A (p.Glu725Lys) results in a conservative amino acid change located in the CFTR regulator domain (IPR025837) 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 0.0001 in 251338 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in CFTR causing Cystic Fibrosis (0.0001 vs 0.013), allowing no conclusion about variant significance. c.2173G>A has been reported in the literature as a non-informative genotype (second allele and/or zygosity not specified or second allele of uncertain/questionable pathogenicity) in individuals with atypical and variably expressive sub-phenotypic or sub clinical presentations of Cystic Fibrosis (CF) (example, Gene_2008, Kanavakis_2003, Larriba_2005, Girardet_2015, Pall_2007, Audrezat_2008, Hekim_2016, Grangeia_2018). These report(s) do not provide unequivocal conclusions about association of the variant with Cystic Fibrosis. Multiple reports of co-occurrences in cis with another pathogenic variant in the CFTR gene (legacy name c.1766+5G>A, also named c.1898+5G>A) with a fully informative genotype in obligate carrier parents and/or CF-chromosomes (Girardet_2015, des Georges_2004) have been reported (ACMG BP2). Additionally, an instance of a co-occurring pathogenic variant in a different gene (SPINK1 c.194+2T>C), in an individual affected with Chronic Pancreatitis (Zou_2018) has also been reported (ACMG BP5). These reports provide supporting evidence for a benign/non-causative role in settings of autosomal recessive Cystic Fibrosis or autosomal dominant SPINK1 associated Pancreatitis. One publication qualitatively reports that double mutants including the variant had no effect on maturation of the CFTR protein (Chen_2002). However, this study does not allow convincing conclusions about the variant effect in isolation. The following publications have been ascertained in the context of this evaluation (PMID: 18687795, 12361483, 18306312, 24762087, 29589582, 27195969, 12752573, 16128988, 17719933, 25735457, 11950844, 30420730, 15698946). Ten submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Multiple submitters reported the variant with conflicting assessments (VUS, n=7; P/LP, n=3). Most submitters cite overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, although this variant meets at-least two supportive criteria given in the ACMG classification guidance, namely BP2 and BP5, the variant was classified as VUS-possibly benign.