ClinVar Genomic variation as it relates to human health

The frequency of this variant in the general population, 0.00011 (14/128988 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant occurs with a second, pathogenic CFTR variant in an individual with congenital bilateral absence of vas deferens (CBVAD) (PMIDs: 21520337 (2011), 10200050 (1998)). Additionally, the variant is reported in individuals with cystic fibrosis (CF) (PMIDs: 34782259 (2021), 26990548 (2016)), chronic bronchitis (PMID: 9921909 (1998)), non-obstructive azoospermia (PMID: 16128988 (2005)), and in healthy individuals (PMID: 24451227 (2014)). Functional studies report the variant slightly destabilizes gene function (PMID: 11278813 (2001)), however further studies are needed. 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. Based on the available information, we are unable to determine the clinical significance of this variant.

The p.P111L variant (also known as c.332C>T), located in coding exon 4 of the CFTR gene, results from a C to T substitution at nucleotide position 332. The proline at codon 111 is replaced by leucine, an amino acid with similar properties. This alteration has been reported with another mutation in association with congenital bilateral absence of vas deferens (de Meeus A et al. Hum. Mutat., 1998;11:480; Steiner B et al. Hum Mutat, 2011 Aug;32:912-20), in the heterozygous state in an individual with chronic bronchitis (Bombieri C et al. Hum. Genet., 1998 Dec;103:718-22), and in the heterozygous state in an individual with non-obstructive azoospermia (Larriba S et al. Int. J. Androl., 2005 Oct;28:284-90). In vitro studies suggested a difference in channel activity between the mutant and wild type under a specific temperature condition (Hämmerle MM et al. J. Biol. Chem., 2001 May;276:14848-54). This amino acid position is highly 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.

ACMG classification criteria: PM2, PM3, PP3

Identified as being possibly associated with CFTR-related disorders, however, functional studies show that this variant only slightly reduced mutant protein biosynthesis, stability, and chloride efflux ability compared to wild type (Hammerle et al., 2001), and several reports of P111L in the published literature describe individuals with non-obstructive azoospermia and chronic bronchitis who were not found to harbor a second CFTR variant in trans (Bombieri et al., 1998; Larriba et al., 2005); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 21520337, 10200050, 26990548, 11278813, 26277102, 29484681, 24727426, 24451227, 9921909, 28603918, 34996830, 33572515, 16128988)

This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 111 of the CFTR protein (p.Pro111Leu). This variant is present in population databases (rs140502196, gnomAD 0.01%). This missense change has been observed in individual(s) with congenital bilateral aplasia of the vas deferens (PMID: 10200050). ClinVar contains an entry for this variant (Variation ID: 53720). 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 expected to disrupt CFTR protein function. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on CFTR function (PMID: 11278813). 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.

This CFTR missense variant has been identified in individuals with features of cystic fibrosis, but not a classic cystic fibrosis phenotype. It (rs140502196) is rare (<0.1%) in a large population dataset (gnomADv4.0.0: 242/1613652 total alleles; 0.015%; no homozygotes) and has an entry in ClinVar (Variation ID: 53720). The proline residue at this position is highly evolutionarily conserved across the species assessed. A single published functional study demonstrates that p.Pro111Leu may have a subtle impact on CFTR protein function and this is supported by an unpublished study that indicates that this variant decreases the conductance of CFTR to a level that is consistent with that of a variant associated with varying clinical consequence. We consider CFTR c.332C>T to be a likely pathogenic variant associated with varying clinical consequence.

The CFTR c.332C>T; p.Pro111Leu variant (rs140502196) is described in the literature in individuals with atypical cystic fibrosis (i.e. congenital bilateral absence of the vas deferens (CBAVD), isolated pulmonary disease) (Bombieri 1998, de Meeus 1998, Larriba 2005). One affected individual carried a second pathogenic variant in CFTR (de Meeus 1998); however, additional pathogenic variants were not identified in other affected individuals (Bombieri 1998, Larriba 2005). The p.Pro111Leu variant is also reported in ClinVar (Variation ID: 53720). This variant is found in the general population with a low overall allele frequency of 0.006% (17/282480 alleles) in the Genome Aggregation Database. The proline at codon 111 is highly conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.842). While functional studies indicate wildtype chloride channel activity at room temperature, this variant exhibits a defect in gating potential at physiological temperatures, suggesting altered activity under conditions closer to those in human tissues (Hammerle 2001). Another variant at the same codon (p.Pro111Ala) exhibits altered gating kinetics (Hammerle 2001) and is reported in an individual with CBAVD who carried a pathogenic variant on the opposite allele (SickKids CFTR database). Although the p.Pro111Leu variant is unlikely to be causative for classic cystic fibrosis, based on available information, we consider it uncertain whether it is pathogenic for other CFTR-related disorders. References: Link to SickKids CFTR database: http://www.genet.sickkids.on.ca/cftr/Home.html Bombieri C et al. Complete mutational screening of the CFTR gene in 120 patients with pulmonary disease. Hum Genet. 1998 Dec;103(6):718-22. PMID: 9921909 de Meeus A et al. Genetic findings in congenital bilateral aplasia of vas deferens patients and identification of six novel mutatations. Mutations in brief no. 138. Online. Hum Mutat. 1998;11(6):480. PMID: 10200050. Hammerle MM 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. PMID: 11278813 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. PMID: 16128988

Variant summary: CFTR c.332C>T (p.Pro111Leu) results in a non-conservative amino acid change located in the ABC transporter type 1, transmembrane domain (IPR011527) 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 6.3e-05 in 252330 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in CFTR causing Congenital Bilateral Absence Of The Vas Deferens/Cystic Fibrosis, allowing no conclusion about variant significance. c.332C>T has been reported in the literature with c.3909C>G(p.Asn1303Lys) in at least one individual affected with Congenital Bilateral Absence Of The Vas Deferens (e.g. deMeeus_1998) and as an uninformative genotype (i.e. zygosity not specified) in a cohort of individuals with positive CF newborn screening results (Bozdogan_2021). These data do not allow any conclusion about variant significance. At least one publication reports experimental evidence evaluating an impact on protein function. These results showed no damaging effect of this variant (Hammerle_2001). The following publications have been ascertained in the context of this evaluation (PMID: 9921909, 16128988, 21520337, 11278813, 10200050, 24451227, 24727426, 33572515). ClinVar contains an entry for this variant (Variation ID: 53720). Based on the evidence outlined above, the variant was classified as uncertain significance.