ClinVar Miner

Submissions for variant NM_024989.4(PGAP1):c.1558A>G (p.Ile520Val)

gnomAD frequency: 0.00003  dbSNP: rs201002323
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000534110 SCV000655085 uncertain significance Intellectual disability, autosomal recessive 42 2022-08-23 criteria provided, single submitter clinical testing 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 sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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. ClinVar contains an entry for this variant (Variation ID: 474990). This variant has not been reported in the literature in individuals affected with PGAP1-related conditions. This variant is present in population databases (rs201002323, gnomAD 0.009%). This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 520 of the PGAP1 protein (p.Ile520Val).
GenomeConnect - Invitae Patient Insights Network RCV003483668 SCV004228688 not provided Intellectual disability, autosomal recessive 58 no assertion provided phenotyping only Variant interpreted as Uncertain significance and reported on 03-26-2020 by Lab Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.

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