ClinVar Miner

Submissions for variant NM_002641.4(PIGA):c.1199G>A (p.Arg400Gln)

gnomAD frequency: 0.00002  dbSNP: rs1921825509
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001297619 SCV001486647 uncertain significance Multiple congenital anomalies-hypotonia-seizures syndrome 2 2020-02-04 criteria provided, single submitter clinical testing 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The glutamine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with PIGA-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces arginine with glutamine at codon 400 of the PIGA protein (p.Arg400Gln). The arginine residue is moderately conserved and there is a small physicochemical difference between arginine and glutamine.
GeneDx RCV001751566 SCV001996770 uncertain significance not provided 2024-11-12 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Revvity Omics, Revvity RCV001751566 SCV003808325 uncertain significance not provided 2019-04-15 criteria provided, single submitter clinical testing

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