ClinVar Miner

Submissions for variant NM_002633.3(PGM1):c.1543C>T (p.Arg515Trp)

gnomAD frequency: 0.00002  dbSNP: rs775651976
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000985040 SCV002268874 uncertain significance PGM1-congenital disorder of glycosylation 2023-08-04 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. This variant disrupts the p.Arg515 amino acid residue in PGM1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 27206562, 33342467). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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 PGM1 protein function. ClinVar contains an entry for this variant (Variation ID: 800856). This variant has not been reported in the literature in individuals affected with PGM1-related conditions. This variant is present in population databases (rs775651976, gnomAD 0.003%). This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 515 of the PGM1 protein (p.Arg515Trp).
Pediatric/Medical Genetics, Ministry of Health, Qatif Central Hospital RCV000985040 SCV003761516 likely pathogenic PGM1-congenital disorder of glycosylation criteria provided, single submitter clinical testing
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center RCV000985040 SCV004807953 uncertain significance PGM1-congenital disorder of glycosylation 2024-03-29 criteria provided, single submitter clinical testing
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City RCV000985040 SCV001132978 uncertain significance PGM1-congenital disorder of glycosylation 2019-08-25 no assertion criteria provided clinical testing

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