ClinVar Miner

Submissions for variant NM_002435.3(MPI):c.61A>G (p.Met21Val)

gnomAD frequency: 0.00006  dbSNP: rs376746368
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000821114 SCV000961858 uncertain significance MPI-congenital disorder of glycosylation 2022-10-17 criteria provided, single submitter clinical testing This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 21 of the MPI protein (p.Met21Val). This variant is present in population databases (rs376746368, gnomAD 0.2%). This variant has not been reported in the literature in individuals affected with MPI-related conditions. ClinVar contains an entry for this variant (Variation ID: 663264). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The valine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.
GeneDx RCV001796255 SCV002032537 uncertain significance not provided 2021-06-04 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant does not alter protein structure/function; In silico analysis, which includes splice predictors and evolutionary conservation, suggests this variant may impact gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; This variant is associated with the following publications: (PMID: 27535533)
Fulgent Genetics, Fulgent Genetics RCV000821114 SCV002776780 uncertain significance MPI-congenital disorder of glycosylation 2021-07-11 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003908109 SCV004724107 likely benign MPI-related disorder 2022-10-24 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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