ClinVar Miner

Submissions for variant NM_015466.4(PTPN23):c.2747A>G (p.Gln916Arg)

gnomAD frequency: 0.00004  dbSNP: rs770692989
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Centre for Mendelian Genomics, University Medical Centre Ljubljana RCV001196789 SCV001367422 uncertain significance Neurodevelopmental disorder and structural brain anomalies with or without seizures and spasticity 2019-12-18 criteria provided, single submitter clinical testing This variant was classified as: Uncertain significance. The available evidence on this variant's pathogenicity is insufficient or conflicting. The following ACMG criteria were applied in classifying this variant: PM2,PP5,BP4.
Invitae RCV001869200 SCV002279076 uncertain significance not provided 2022-09-27 criteria provided, single submitter clinical testing This sequence change replaces glutamine, which is neutral and polar, with arginine, which is basic and polar, at codon 916 of the PTPN23 protein (p.Gln916Arg). This variant is present in population databases (rs770692989, gnomAD 0.007%). This missense change has been observed in individual(s) with clinical features of PTPN23-related conditions (PMID: 31395947). ClinVar contains an entry for this variant (Variation ID: 636314). 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: "Tolerated"; PolyPhen-2: "Not Available"; 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.
Regeneron Genetics Center, Regeneron RCV000853201 SCV000927108 likely pathogenic Global developmental delay; Brain atrophy 2019-02-15 no assertion criteria provided research Identified in cohort of patients with neurodevelopmental disorder accompanied by structural brain abnormalities

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