ClinVar Miner

Submissions for variant NM_000303.3(PMM2):c.337C>A (p.Pro113Thr)

dbSNP: rs765433263
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000482436 SCV000569753 likely pathogenic not provided 2024-07-12 criteria provided, single submitter clinical testing Identified with a second variant in PMM2 in a patient in published literature; detailed clinical information and segregation was not reported (PMID: 37224763); 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: 37224763)
Labcorp Genetics (formerly Invitae), Labcorp RCV000984293 SCV003491859 likely pathogenic PMM2-congenital disorder of glycosylation 2023-02-14 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 113 of the PMM2 protein (p.Pro113Thr). This variant is present in population databases (rs765433263, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with PMM2-related conditions. ClinVar contains an entry for this variant (Variation ID: 420784). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PMM2 protein function. This variant disrupts the p.Pro113 amino acid residue in PMM2. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 9140401, 11058895, 18948042, 21541725). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Counsyl RCV000984293 SCV001132462 uncertain significance PMM2-congenital disorder of glycosylation 2019-01-24 no assertion criteria provided clinical testing
PreventionGenetics, part of Exact Sciences RCV004755929 SCV005342091 likely pathogenic PMM2-related disorder 2024-09-05 no assertion criteria provided clinical testing The PMM2 c.337C>A variant is predicted to result in the amino acid substitution p.Pro113Thr. This variant has been reported in the presumed compound heterozygous state with a PMM2 nonsense variant (c.109C>T, p.Gln37*) in an individual with congenital disorder of glycosylation type 1a (PMM2-CDG) (Table 2, De Graef et al. 2023. PubMed ID: 37224763). This variant is reported in 0.0029% of alleles (1 of 34,590) in individuals of Latino descent in gnomAD. Of note, another missense variant affecting the same amino acid residue (p.Pro113Leu) has been reported in multiple individuals with PMM2-CDG and shown to cause a loss of function (Matthijs et al. 1997. PubMed ID: 9140401; Vega et al. 2011. PubMed ID: 21541725; Yuste-Checa et al. 2015. PubMed ID: 26014514; Segovia-Falquina et al. 2022. PubMed ID: 35789514). Taken together, the p.Pro113Thr variant is interpreted as likely pathogenic.

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