ClinVar Miner

Submissions for variant NM_080605.4(B3GALT6):c.31C>T (p.Arg11Trp) (rs1039242906)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000444888 SCV000528170 uncertain significance not provided 2016-05-17 criteria provided, single submitter clinical testing The R11W variant in the B3GALT6 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. Data from control individuals were not available to assess whether R11W may be a common benign variant in the general population. The R11W 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. This substitution occurs at a position that is conserved in mammals. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. However, a missense variants in a nearby residue (R6W) has been reported in the Human Gene Mutation Database in association with EDSP2 (Stenson et al., 2014), supporting the functional importance of this region of the protein. We interpret R11W as a variant of uncertain significance.
Invitae RCV001064480 SCV001229385 uncertain significance Ehlers-Danlos syndrome, progeroid type, 2; Spondyloepimetaphyseal dysplasia with joint laxity 2019-11-20 criteria provided, single submitter clinical testing This sequence change replaces arginine with tryptophan at codon 11 of the B3GALT6 protein (p.Arg11Trp). The arginine residue is moderately conserved and there is a moderate physicochemical difference between arginine and tryptophan. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This variant has not been reported in the literature in individuals with B3GALT6-related conditions. ClinVar contains an entry for this variant (Variation ID: 386485). 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.

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