ClinVar Miner

Submissions for variant NM_000303.3(PMM2):c.647A>G (p.Asn216Ser)

gnomAD frequency: 0.00001  dbSNP: rs78290141
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000485565 SCV000568194 uncertain significance not provided 2024-12-13 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 11142762, 11409861, 11058895, 11058896, 34859900, 28122681, 37002680)
Baylor Genetics RCV000675138 SCV001527207 likely pathogenic PMM2-congenital disorder of glycosylation 2024-02-17 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000485565 SCV002520058 likely pathogenic not provided 2021-10-25 criteria provided, single submitter clinical testing PP3, PP4, PM2, PM5
Labcorp Genetics (formerly Invitae), Labcorp RCV000675138 SCV003522707 pathogenic PMM2-congenital disorder of glycosylation 2025-01-05 criteria provided, single submitter clinical testing This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 216 of the PMM2 protein (p.Asn216Ser). This variant is present in population databases (rs78290141, gnomAD 0.004%). This missense change has been observed in individual(s) with congenital disorder of glycosylation (PMID: 11058896, 28122681). ClinVar contains an entry for this variant (Variation ID: 198713). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt PMM2 protein function with a positive predictive value of 95%. This variant disrupts the p.Asn216 amino acid residue in PMM2. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 9140401, 11875054, 25355454). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
Fulgent Genetics, Fulgent Genetics RCV000675138 SCV005642481 likely pathogenic PMM2-congenital disorder of glycosylation 2024-04-05 criteria provided, single submitter clinical testing
Eurofins Ntd Llc (ga) RCV000485565 SCV000232515 uncertain significance not provided 2014-06-10 flagged submission clinical testing
Counsyl RCV000675138 SCV000800726 uncertain significance PMM2-congenital disorder of glycosylation 2017-09-26 flagged submission clinical testing
Natera, Inc. RCV000675138 SCV001457179 likely pathogenic PMM2-congenital disorder of glycosylation 2020-09-16 no assertion criteria provided clinical testing

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