ClinVar Miner

Submissions for variant NM_002633.3(PGM1):c.1258T>C (p.Tyr420His)

gnomAD frequency: 0.21027  dbSNP: rs11208257
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000367456 SCV000358650 benign Congenital disorder of glycosylation 2016-06-14 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000277905 SCV000358651 benign PGM1-congenital disorder of glycosylation 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
GeneDx RCV000419125 SCV000517631 benign not specified 2015-12-02 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV000277905 SCV001722696 benign PGM1-congenital disorder of glycosylation 2024-02-01 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000277905 SCV002048022 benign PGM1-congenital disorder of glycosylation 2023-11-29 criteria provided, single submitter clinical testing
Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan RCV000419125 SCV004233250 benign not specified 2024-01-24 criteria provided, single submitter clinical testing This variant is classified as Benign based on local population frequency. This variant was detected in 60% of patients studied by a panel of primary immunodeficiencies. Number of patients: 57. Only high quality variants are reported.
Mayo Clinic Laboratories, Mayo Clinic RCV000675306 SCV000800971 benign not provided 2015-10-23 no assertion criteria provided clinical testing

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