Variant summary: CFTR c.3908A>T (p.Asn1303Ile) results in a non-conservative amino acid change located in the ABC transporter-like, ATP-binding domain (IPR003439) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4.8e-05 in 249628 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in CFTR causing Cystic Fibrosis (4.8e-05 vs 0.013), allowing no conclusion about variant significance. c.3908A>T has been reported in the literature in at-least two individuals affected with Cystic Fibrosis and Congenital Bilateral Absence of the Vas Deferens (example, Clausters_2000). These data indicate that the variant may be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in a long burst duration and a long interburst interval of CFTR gating via patch-clamp electrophysiology (Berger_2002). Additionally, other variants at the Asn1303 residue have been reported as associated with disease (p.Asn1303Lys), suggesting that this codon is functionally important. The following publications have been ascertained in the context of this evaluation (PMID: 11788611, 10923036, 21520337). ClinVar contains an entry for this variant (Variation ID: 53846). Based on the evidence outlined above, the variant was classified as likely pathogenic.

This sequence change replaces asparagine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 1303 of the CFTR protein (p.Asn1303Ile). This variant is present in population databases (rs397508636, gnomAD 0.02%). This missense change has been observed in individuals with CFTR-related conditions (PMID: 9598638, 10923036). ClinVar contains an entry for this variant (Variation ID: 53846). 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: 11788611). This variant disrupts the p.Asn1303 amino acid residue in CFTR. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 21520337, 23951356, 23974870). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

This variant was identified in 1 patient with a clinically confirmed diagnosis of cystic fibrosis. The variant was classified in the context of a project re-classifying variants in the German Cystic Fibrosis Registry (Muko.e.V.). Link: https://www.muko.info/angebote/qualitaetsmanagement/register/cf-einrichtungen/mukoweb. Criteria applied: PS3_SUP, PM2_SUP, PM3, PM5_STR, PP3

Absent from controls (or at extremely low frequency if recessive) in Genome Aggregation Database, Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium.;Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.;For recessive disorders, detected in trans with a pathogenic variant.;Patient's phenotype or family history is highly specific for a disease with a single genetic etiology.;Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.

The c.3908A>T variant in CFTR is a missense variant predicted to cause substitution of asparagine to isoleucine at amino acid 1303. This variant is rare in the general population with a frequency below the threshold expected for the associated phenotype(s). This variant has been observed in one or more individuals affected with the associated recessive disease, as either homozygous or compound heterozygous with a second variant (PMID: 39482189). Functional studies show that this variant may disrupt protein function (PMID: 38388235). A different variant at the same position has been determined to be Pathogenic or Likely Pathogenic. Computational prediction algorithms indicate this variant is likely to affect gene or protein function. Given the available evidence, this variant is classified as Likely Pathogenic.

The p.N1303I variant (also known as c.3908A>T), located in coding exon 24 of the CFTR gene, results from an A to T substitution at nucleotide position 3908. The asparagine at codon 1303 is replaced by isoleucine, 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 (Ambry internal data). 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 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 the majority of available evidence to date, this variant is likely to be pathogenic.