ClinVar Genomic variation as it relates to human health

The p.D565G variant (also known as c.1694A>G), located in coding exon 13 of the CFTR gene, results from an A to G substitution at nucleotide position 1694. The aspartic acid at codon 565 is replaced by glycine, an amino acid with similar properties. This variant has been identified in several individuals with symptoms of cystic fibrosis or CFTR-related disorders in conjunction with p.R668C; in some individuals, these variants were shown to occur in cis (Kanavakis E et al. Mol Hum Reprod, 1998 Apr;4:333-7; Pagani F et al. Hum Mol Genet, 2003 May;12:1111-20). Analysis of exon skipping in 12 individuals with p.R688C in cis demonstrated increased exon skipping compared to controls in half, with the remaining half with similar levels to controls (Pagani F et al. Hum Mol Genet, 2003 May;12:1111-20). This amino acid position is highly conserved in available vertebrate species. In silico splice site analysis for this alteration is inconclusive. In addition, as a missense substitution this 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.

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

This sequence change replaces aspartic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 565 of the CFTR protein (p.Asp565Gly). 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 conditions (PMID: 9620832, 21520337). ClinVar contains an entry for this variant (Variation ID: 53344). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. Studies have shown that this variant is associated with altered splicing, but the impact on the resulting protein product is unknown (PMID: 12719375). 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.

Variant summary: CFTR c.1694A>G (p.Asp565Gly) results in a non-conservative amino acid change to a highly conserved residue (HGMD) located in the 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 was absent in 250396 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.1694A>G has been reported in the literature in a heterozygous state in individuals affected with congenital bilateral absence of the vas deferens (CBAVD), disseminated bronchiectasis, pneumonia, nasal polyps, idiopathic chronic pancreatitis, and cystic fibrosis, but was also found in multiple unaffected individuals (e.g. Kanavakis_1998, Tzetis_2001, Pagani_2003, Steiner_2011, Raraigh_2022). In several of these cases and controls the variant was noted to co-occur in complex (i.e. in cis) with the c.2002C>T (p.Arg668Cys) variant (Pagani_2003). In addition, the variant was also reported in an individual affected with assumed CBAVD (i.e. obstructive azoospermia), who also carried a common pathogenic variant (Ooi_2014), however in this patient sweat chloride concentration was below 60 mmol/L, and nasal potential difference (NPD) was indicated to be normal. These data do not allow any conclusion about variant significance. At least one publication reported experimental evidence, and demonstrated that it resulted in a partial exon skipping in nasal epithelial cells derived from individuals carrying the variant, as well as in an in vitro minigene system (Pagani_2003). The variant might affect exonic splicing regulatory elements, as the extent of the splicing defect caused by the D565G variant in the minigene system was highly dissimilar among the five transfected cell lines, and the degree of splice defect was also heavily influenced by the co-transfection of various splicing factors (Pagani_2003). Therefore, these data do not allow clear conclusions about the variant effect in vivo. The following publications have been ascertained in the context of this evaluation (PMID: 12719375, 18456578, 21520337, 11810271, 9620832, 24697796, 17076271, 34782259). Six submitters have cited clinical-significance assessments for this variant to ClinVar after 2014, and classified it as uncertain significance (n=4) or pathogenic/likely pathogenic (n=2). Based on the evidence outlined above, the variant was classified as uncertain significance.