ClinVar Miner

Submissions for variant NM_032634.4(PIGO):c.484A>G (p.Asn162Asp)

gnomAD frequency: 0.00001  dbSNP: rs776095449
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000493352 SCV000582799 uncertain significance not provided 2017-05-16 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the PIGO gene. The N162D variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The N162D variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The N162D variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. Based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Centogene AG - the Rare Disease Company RCV001809450 SCV002059763 uncertain significance Hyperphosphatasia with intellectual disability syndrome 2 2019-04-24 criteria provided, single submitter clinical testing
Invitae RCV001809450 SCV002160393 uncertain significance Hyperphosphatasia with intellectual disability syndrome 2 2021-09-24 criteria provided, single submitter clinical testing This sequence change replaces asparagine with aspartic acid at codon 162 of the PIGO protein (p.Asn162Asp). The asparagine residue is highly conserved and there is a small physicochemical difference between asparagine and aspartic acid. This variant is present in population databases (rs776095449, ExAC 0.009%). This missense change has been observed in individual(s) with clinical features of PIGO-congenital disorder of glycosylation (Invitae). ClinVar contains an entry for this variant (Variation ID: 430076). 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: "Probably 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.

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