ClinVar Miner

Submissions for variant NM_152490.5(B3GALNT2):c.169G>A (p.Val57Met) (rs142756842)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genomic Research Center,Shahid Beheshti University of Medical Sciences RCV000557432 SCV000746552 likely pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 2017-12-03 criteria provided, single submitter clinical testing
Invitae RCV000557432 SCV000653536 uncertain significance Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 2016-09-27 criteria provided, single submitter clinical testing This sequence change replaces valine with methionine at codon 57 of the B3GALNT2 protein (p.Val57Met). The valine residue is highly conserved and there is a small physicochemical difference between valine and methionine. This variant is present in population databases (rs142756842, ExAC 0.04%) but has not been reported in the literature in individuals with a B3GALNT2-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). The methionine amino acid residue is also found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies. In summary, this variant is a rare missense change with uncertain impact on protein function. Because it is found in the population at an appreciable frequency, this variant is not anticipated to cause disease. However, the available evidence is currently insufficient to prove that conclusively. Therefore, it has been classified as a Variant of Uncertain Significance.

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