ClinVar Genomic variation as it relates to human health

The CFTR c.346G>A; p.Glu116Lys variant (rs397508571) has been described in the compound heterozygous state in individuals with mild cystic fibrosis and allergic bronchopulmonary aspergillosis, and in the homozygous state in one individual with a CFTR-related disorder with unknown clinical phenotype (see link to SickKids database, Burgel 2010, Schrijver 2005). It is absent from general population databases (1000 Genomes Project, Exome Variant Server, and Genome Aggregation Database), indicating it is not a common polymorphism. The glutamic acid at codon 116 is highly conserved, but computational algorithms (PolyPhen-2: probably damaging, SIFT: tolerated) are inconclusive on the effects of this variant on protein structure and/or function. Functional studies demonstrate destabilization of the open state of the chloride channel and slightly reduced transport of mature CFTR protein to the cell surface (Hammerle 2001). Based on available information, this variant is considered likely pathogenic. References: SickKids Databse: http://www.genet.sickkids.on.ca/cftr/MutationDetailPage.external?sp=87 Burgel P et al. Non-classic cystic fibrosis associated with D1152H CFTR mutation. Clin Genet. 2010 Apr;77(4):355-64. Hammerle M et al. Disease-associated mutations in the extracytoplasmic loops of cystic fibrosis transmembrane conductance regulator do not impede biosynthetic processing but impair chloride channel stability. J Biol Chem. 2001 May 4;276(18):14848-54. 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.

the variant causes a phenotype but regarding our data, we can't formally attribute it to CF, CFTR-RD or both

The p.E116K variant (also known as c.346G>A), located in coding exon 4 of the CFTR gene, results from a G to A substitution at nucleotide position 346. The glutamic acid at codon 116 is replaced by lysine, an amino acid with similar properties. This pathogenic alteration was described in the homozygous state in one individual in a Hispanic population, but specific clinical information was not reported (Schrijver et al. J Mol Diagn 2005 May; 7(2):289-99 ). In vitro studies demonstrated that this alteration affects protein chloride channel current and transport to the cell membrane (Cui et al. J Gen Physiol. 2014;144(2):159-79; Hammerle et al. J. Biol. Chem. 2001 May; 276(18):14848-54; Lu et al. J. Biol. Chem. 1998 Jan; 273(1):568-76). In addition, this variant has been detected in conjunction with a pathogenic alteration in CFTR several times by our laboratory to date. This variant is unknown to be in cis or trans with these known pathogenic alterations. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6503 samples (13006 alleles) with coverage at this position. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be probably damaging and tolerated by PolyPhen and SIFT in silico analyses, respectively. Based on the majority of available evidence to date, this variant is likely to be pathogenic.

This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 116 of the CFTR protein (p.Glu116Lys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of cystic fibrosis (PMID: 15858154, 19843100; internal data). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 53754). 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%. Experimental studies have shown that this missense change affects CFTR function (PMID: 11278813, 29805046, 30046002). For these reasons, this variant has been classified as Pathogenic.

Variant summary: CFTR c.346G>A (p.Glu116Lys) results in a conservative amino acid change located in the ABC transporter type 1, transmembrane domain (IPR011527) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251008 control chromosomes. c.346G>A has been reported in the literature in a homozygous patient suspected of Cystic Fibrosis (Schrijver_2005) and compound heterozygous patients with Cystic Fibrosis and related conditions (Brugel_2010 and Sickkids_database). These data indicate that the variant is likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function demonstrating reduced transport of mature CFTR protein to cell surface and destabalization of the open state of chloride channel (Hammerle_2001) and severely reduced functionality (Raraigh_2018). The following publications have been ascertained in the context of this evaluation (PMID: 19843100, 11278813, 30888834, 29805046, 15858154, Sickkids_database).Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic (n=3) and likely pathogenic (n=3). Based on the evidence outlined above, the variant was classified as pathogenic.