Total submissions: 2
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Gene |
RCV000486578 | SCV000574217 | uncertain significance | not specified | 2017-03-20 | criteria provided, single submitter | clinical testing | The c.1777G>C variant in the PIK3CD gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The c.1777G>C variant is observed in 11/65934 (0.02%) alleles from individuals of European background, in the ExAC dataset (Lek et al., 2016). In silico splice prediction models predict that c.1777G>C may create a cryptic splice donor site in exon 14, however this variant is not predicted to affect the natural splice donor site. In the absence of RNA/functional studies, the actual effect of the c.1777G>C change in this individual is unknown. If c.1777G>C does not alter splicing, it will result in the G593R missense change. The G593R variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved in mammals. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret c.1777G>C as a variant of uncertain significance. |
| Labcorp Genetics |
RCV000651286 | SCV000773137 | uncertain significance | Immunodeficiency 14 | 2024-01-18 | criteria provided, single submitter | clinical testing | This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 593 of the PIK3CD protein (p.Gly593Arg). This variant is present in population databases (rs143068130, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with PIK3CD-related conditions. ClinVar contains an entry for this variant (Variation ID: 424409). 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 not expected to disrupt PIK3CD protein function with a negative predictive value of 80%. 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. |