ClinVar Miner

Submissions for variant NM_176787.5(PIGN):c.1766A>G (p.Lys589Arg)

gnomAD frequency: 0.00009  dbSNP: rs775932562
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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 RCV000690571 SCV000818261 uncertain significance Multiple congenital anomalies-hypotonia-seizures syndrome 1 2022-11-01 criteria provided, single submitter clinical testing This sequence change replaces lysine, which is basic and polar, with arginine, which is basic and polar, at codon 589 of the PIGN protein (p.Lys589Arg). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with PIGN-related conditions. ClinVar contains an entry for this variant (Variation ID: 569845). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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.
Ambry Genetics RCV002397391 SCV002711781 uncertain significance Inborn genetic diseases 2024-10-24 criteria provided, single submitter clinical testing The c.1766A>G (p.K589R) alteration is located in exon 19 (coding exon 16) of the PIGN gene. This alteration results from a A to G substitution at nucleotide position 1766, causing the lysine (K) at amino acid position 589 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Revvity Omics, Revvity RCV000690571 SCV003808347 uncertain significance Multiple congenital anomalies-hypotonia-seizures syndrome 1 2022-06-02 criteria provided, single submitter clinical testing

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