ClinVar Miner

Submissions for variant NM_005026.5(PIK3CD):c.1002C>G (p.Asn334Lys)

dbSNP: rs28730670
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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000701558 SCV000830364 pathogenic Immunodeficiency 14 2023-12-11 criteria provided, single submitter clinical testing This sequence change replaces asparagine, which is neutral and polar, with lysine, which is basic and polar, at codon 334 of the PIK3CD protein (p.Asn334Lys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of activated PIK3 delta syndrome (PMID: 24165795, 35753512; Invitae; external communication). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 578525). 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 PIK3CD protein function with a positive predictive value of 80%. This variant disrupts the p.Asn334 amino acid residue in PIK3CD. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 24165795, 28167755). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

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