ClinVar Miner

Submissions for variant NM_032634.4(PIGO):c.1549G>A (p.Ala517Thr)

gnomAD frequency: 0.00001  dbSNP: rs781222643
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001227763 SCV001400134 uncertain significance Hyperphosphatasia with intellectual disability syndrome 2 2021-08-24 criteria provided, single submitter clinical testing This sequence change replaces alanine with threonine at codon 517 of the PIGO protein (p.Ala517Thr). The alanine residue is moderately conserved and there is a small physicochemical difference between alanine and threonine. This variant is present in population databases (rs781222643, ExAC 0.003%). This variant has not been reported in the literature in individuals affected with PIGO-related conditions. 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"). 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.
GeneDx RCV001773518 SCV002001351 uncertain significance not provided 2021-01-04 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); 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
Ambry Genetics RCV004032615 SCV005005604 uncertain significance Inborn genetic diseases 2023-12-16 criteria provided, single submitter clinical testing The c.1549G>A (p.A517T) alteration is located in exon 7 (coding exon 6) of the PIGO gene. This alteration results from a G to A substitution at nucleotide position 1549, causing the alanine (A) at amino acid position 517 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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