ClinVar Miner

Submissions for variant NM_005026.5(PIK3CD):c.598G>A (p.Glu200Lys)

gnomAD frequency: 0.00028  dbSNP: rs141200414
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000795754 SCV000935227 uncertain significance Immunodeficiency 14 2024-11-25 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 200 of the PIK3CD protein (p.Glu200Lys). This variant is present in population databases (rs141200414, gnomAD 0.05%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with PIK3CD-related conditions (internal data). ClinVar contains an entry for this variant (Variation ID: 642308). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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.
CeGaT Center for Human Genetics Tuebingen RCV000993900 SCV001147124 uncertain significance not provided 2019-02-01 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002501049 SCV002813344 uncertain significance Combined immunodeficiency with faciooculoskeletal anomalies; Immunodeficiency 14; Immunodeficiency 14b, autosomal recessive 2021-10-14 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000993900 SCV004563926 uncertain significance not provided 2023-09-18 criteria provided, single submitter clinical testing
Rarefied Biosciences Lab RCV004813140 SCV005423719 likely pathogenic Activated PI3K-delta syndrome no assertion criteria provided research p.Glu200Lys is classified here as likely pathogenic due to experimental evidence showing gain of mTOR function. The proportion of circulating transitional B cells is higher as compared to healthy controls. The proportion of TFH is normal compared to controls.

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