ClinVar Miner

Submissions for variant NM_032634.4(PIGO):c.2092G>A (p.Glu698Lys)

gnomAD frequency: 0.00003  dbSNP: rs571768342
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000709821 SCV002310111 uncertain significance Hyperphosphatasia with intellectual disability syndrome 2 2021-09-21 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid with lysine at codon 698 of the PIGO protein (p.Glu698Lys). The glutamic acid residue is moderately conserved and there is a small physicochemical difference between glutamic acid and lysine. This variant is present in population databases (rs571768342, ExAC 0.07%). 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: 585062). 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.
Ambry Genetics RCV002534481 SCV003550223 likely benign Inborn genetic diseases 2021-07-06 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
GenomeConnect, ClinGen RCV000709821 SCV000840150 not provided Hyperphosphatasia with intellectual disability syndrome 2 no assertion provided phenotyping only Variant interpreted as Uncertain significance and reported on 01-24-2019 by Lab or GTR ID 500105. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

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