ClinVar Miner

Submissions for variant NM_032634.4(PIGO):c.2995C>T (p.Arg999Trp)

gnomAD frequency: 0.00001  dbSNP: rs61746764
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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 RCV001054686 SCV001219034 uncertain significance Hyperphosphatasia with intellectual disability syndrome 2 2022-11-01 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 999 of the PIGO protein (p.Arg999Trp). 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 missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 850506). This variant has not been reported in the literature in individuals affected with PIGO-related conditions. This variant is present in population databases (rs61746764, gnomAD 0.006%).
GeneDx RCV002466616 SCV002762598 uncertain significance not provided 2022-12-09 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV004031725 SCV005005616 uncertain significance Inborn genetic diseases 2024-02-12 criteria provided, single submitter clinical testing The c.2995C>T (p.R999W) alteration is located in exon 9 (coding exon 8) of the PIGO gene. This alteration results from a C to T substitution at nucleotide position 2995, causing the arginine (R) at amino acid position 999 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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