Variant summary: CFTR c.2552G>T (p.Arg851Leu) results in a non-conservative amino acid change in the encoded protein sequence. Algorithms developed to predict the effect of missense changes on protein structure and function all suggest that this variant is likely to be disruptive. The variant was absent in 251312 control chromosomes. The variant, c.2552G>T, has been reported in the literature in compound heterozygosity with p.F508del in an individual with idiopathic chronic pancreatitis and bronchitis (Bernardino_2003), and in an individual with congenital bilateral absence of the vas deferens (CBAVD) and a sweat chloride of 74 mmol/L (de la Taille_1998); in a third individual who had diffuse bronchiectasis, but was reported with normal sweat chloride value, the variant was found in compound heterozygosity with p.Arg553* (Bienvenu_2010). The variant was also reported in homozygous state in an individual diagnosed with CFTR-RD (Trujillano_2013). In addition, the variant allele was found in individuals diagnosed cystic fibrosis (CF) or CF-related phenotypes (e.g. Claustres_2000, Perez_2007, da Silva Filho_2020), however in these patients the second allele was not specified. Lastly, a case of "presumed" homozygosity in two children from a consanguineous family who reportedly died due to CF (therefore, not genotyped) has been reported (Casals_1997). 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. The most pronounced variant effect resulted in <10% of normal chloride channel conductance relative to wild type (e.g., Bihler_2024). The following publications have been ascertained in the context of this evaluation (PMID: 17331079, 14526128, 20167849, 9439669, 10923036, 27086061, 16963320, 23687349, 32819855, 9598638, 38388235). ClinVar contains an entry for this variant (Variation ID: 53511). Based on the evidence outlined above, the variant was classified as pathogenic.

The p.R851L pathogenic mutation (also known as c.2552G>T), located in coding exon 15 of the CFTR gene, results from a G to T substitution at nucleotide position 2552. The arginine at codon 851 is replaced by leucine, an amino acid with dissimilar properties. This variant has been identified in the homozygous state and/or in conjunction with other CFTR variant(s) in individual(s) with features consistent with cystic fibrosis or CFTR-related disorders; in at least one instance, the variants were identified in trans (Bernardino AL et al. Genet Test, 2000;4:69-74; Bienvenu T et al. Am J Respir Crit Care Med, 2010 May;181:1078-84; Trujillano D et al. J Med Genet, 2013 Jul;50:455-62; Gaitch N et al. Pancreatology, 2016 Apr;16:515-22). In an assay testing CFTR function, this variant showed a functionally abnormal result (Bihler H et al. J Cyst Fibros, 2024 Jul;23:664-675). This nucleotide position is well conserved in available vertebrate species. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this variant is interpreted as a disease-causing mutation.

This sequence change replaces arginine, which is basic and polar, with leucine, which is neutral and non-polar, at codon 851 of the CFTR protein (p.Arg851Leu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of CFTR-related disease (PMID: 9598638, 20167849, 27086061). 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: 53511). 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.

This variant was first described in a carrier father who had two deceased children who died from Cystic Fibrosis (CF), and these kids were probably homozygous to this variant (due to parent consanguinity). However, that has never been confirmed (Casals et al. 1997). This imprecision led to the belief that this variant is pathogenic. Despite this variant has been classified and reclassified over the course of time as pathogenic and lately as likely pathogenic (by Mendelics and Invitae), new functional evidence has shown that this variant does not alter CFTR function even when located in the same allele (in cis) as NM_000492.4(CFTR):1052C>G; p.Thr351Ser) and in trans with the most common pathogenic variant p.Phe508del (NM_000492.4(CFTR):1521_1523delCTT). Although in a pathogenic range due to its very low frequency in public databases (absent in ExAc but seen twice in GnomAd (in a non-Finnish European and in a person of unknown ethnicity), the aminoacid change promoted by this missense variant is located in the transition between the cytoplasm and the transmembrane portions of CFTR, at the beginning of the second transmembrane domain, which does not implicate in an abrupt abnormality in the CFTR protein. Also, there is another missense variant in the same nucleotide position which has been classified as having uncertain significance (NM_000492.4(CFTR):c.2552G>A; p.Arg851Gln). Besides, prediction tools are very disagreeable when predicting the deleteriousness of this variant. Therefore, the controversial data existing to date regarding this variant leads to the classification of uncertain significance. Brief Medical History: the patient was diagnosed with NBS and treated with pancreatic enzymes until the age of 2-3 y.o. The mother decided to stop giving any medication. Since then, the patient presented normal thrive and growth, normal stature, and was eutrophic throughout her life, which would not be expected given the patient's genotype. The patient is now 22 y.o. and has no history of chronic lung infections nor exacerbations or any other features compatible with Cystic Fibrosis. Sweat chloride tests have always been within borderline range (30-59 mM). Also, the patient is pancreatic-sufficient. In January 2020, the patient provided stool samples. Fecal elastase-1 levels in feces samples are within the normal range of the assay, which is a biomarker of pancreatic exocrine sufficiency. Other biochemical and hematological measurements to verify liver function were also normal throughout the patient's life.