ClinVar Miner

Submissions for variant NM_032634.4(PIGO):c.253C>A (p.Pro85Thr)

gnomAD frequency: 0.00013  dbSNP: rs745754359
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000525770 SCV000652689 uncertain significance Hyperphosphatasia with intellectual disability syndrome 2 2022-08-21 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 85 of the PIGO protein (p.Pro85Thr). This variant is present in population databases (rs745754359, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with PIGO-related conditions. ClinVar contains an entry for this variant (Variation ID: 473224). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest 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.
GeneDx RCV001577557 SCV001804956 uncertain significance not provided 2022-07-06 criteria provided, single submitter clinical testing 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; This variant is associated with the following publications: (PMID: 24417746)
Ambry Genetics RCV003302869 SCV003992532 uncertain significance Inborn genetic diseases 2023-04-11 criteria provided, single submitter clinical testing The c.253C>A (p.P85T) alteration is located in exon 2 (coding exon 1) of the PIGO gene. This alteration results from a C to A substitution at nucleotide position 253, causing the proline (P) at amino acid position 85 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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