ClinVar Miner

Submissions for variant NM_005027.4(PIK3R2):c.1042C>A (p.Pro348Thr)

gnomAD frequency: 0.00001  dbSNP: rs368358984
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001754713 SCV001996290 uncertain significance not provided 2019-09-30 criteria provided, single submitter clinical testing In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge
Labcorp Genetics (formerly Invitae), Labcorp RCV001868427 SCV002200683 uncertain significance Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1 2024-03-08 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 348 of the PIK3R2 protein (p.Pro348Thr). This variant is present in population databases (rs368358984, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with PIK3R2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1308825). 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 PIK3R2 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.

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