ClinVar Miner

Submissions for variant NM_020964.3(EPG5):c.6166C>T (p.Arg2056Trp) (rs116076204)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000421782 SCV000535413 uncertain significance not provided 2017-01-13 criteria provided, single submitter clinical testing The R2056W variant in the EPG5 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. Although not reported in the homozygous state, the R2056W variant was observed at a frequency of 1.1%, 45/3988 alleles, in individuals of African American ancestry by the NHLBI Exome Sequencing Project. The R2056W 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 not conserved. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret R2056W as a variant of uncertain significance.
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV000768206 SCV000898667 uncertain significance Vici syndrome 2017-12-18 criteria provided, single submitter clinical testing EPG5 NM_020964.2 exon 36 p.Arg2056Trp (c.6166C>T): This variant has not been reported in the literature but is present in 0.8% (199/24018) of African alleles, including 1 homozygote in the Genome Aggregation Database (http://gnomad.broadinstitute.org/rs116076204). This variant is present in ClinVar (Variation ID:392189). Evolutionary conservation and computational predictive tools suggest that this variant may not impact the protein. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
Invitae RCV000768206 SCV001035464 likely benign Vici syndrome 2019-12-31 criteria provided, single submitter clinical testing

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