ClinVar Miner

Submissions for variant NM_152490.5(B3GALNT2):c.410C>T (p.Ser137Leu) (rs140393851)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000731342 SCV000621753 uncertain significance not provided 2017-10-25 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the B3GALNT2 gene. The S137L variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The S137L variant is observed in 20/34410 (0.06%) alleles from individuals of Latino background (Lek et al., 2016). The S137L variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. However, this substitution occurs at a position that is not conserved; and in silico analysis predicts this variant likely does not alter the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Invitae RCV000527424 SCV000653542 uncertain significance Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 2019-12-23 criteria provided, single submitter clinical testing This sequence change replaces serine with leucine at codon 137 of the B3GALNT2 protein (p.Ser137Leu). The serine residue is weakly conserved and there is a large physicochemical difference between serine and leucine. This variant is present in population databases (rs140393851, ExAC 0.06%). This variant has not been reported in the literature in individuals with B3GALNT2-related disease. ClinVar contains an entry for this variant (Variation ID: 452907). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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.
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000731342 SCV000859148 uncertain significance not provided 2018-01-25 criteria provided, single submitter clinical testing

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