ClinVar Miner

Submissions for variant NM_000303.3(PMM2):c.634A>G (p.Met212Val)

gnomAD frequency: 0.00014  dbSNP: rs3743808
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000780610 SCV000918026 benign not specified 2021-08-24 criteria provided, single submitter clinical testing Variant summary: PMM2 c.634A>G (p.Met212Val) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00052 in 396268 control chromosomes, predominantly at a frequency of 0.0086 within the East Asian subpopulation in the gnomAD database (v2.1 and v3.1 datasets), including 1 homozygote. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 1.54 fold of the estimated maximal expected allele frequency for a pathogenic variant in PMM2 causing Congenital Disorder of Glycosylation Type 1a phenotype (0.0056). However, the variant was reported in some East Asian subpopulations with an even higher allele frequency, e.g. in the Japanese, with an allele frequency of 0.026 (in the jMorp database). This frequency is about 4.6-fold higher than the maximum expected for a pathogenic variant, strongly suggesting that the variant is a benign polymorphism found primarily in populations of East Asian origin. Though the variant, c.634A>G, has been reported in the literature in an East Asian individual affected with Congenital Disorder of Glycosylation Type 1a (Ren_2015), this report does not provide unequivocal conclusions about association of the variant with Congenital Disorder of Glycosylation Type 1a. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as likely benign, while the other laboratory classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as benign.
Invitae RCV000877159 SCV001019851 likely benign PMM2-congenital disorder of glycosylation 2021-12-17 criteria provided, single submitter clinical testing
Illumina Laboratory Services,Illumina RCV000877159 SCV001274416 uncertain significance PMM2-congenital disorder of glycosylation 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Genetic Services Laboratory,University of Chicago RCV000780610 SCV002070549 likely benign not specified 2018-12-31 criteria provided, single submitter clinical testing
Natera, Inc. RCV000877159 SCV002089492 likely benign PMM2-congenital disorder of glycosylation 2020-01-16 no assertion criteria provided clinical testing

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