ClinVar Miner

Submissions for variant NM_020458.4(TTC7A):c.59G>A (p.Cys20Tyr)

gnomAD frequency: 0.00002  dbSNP: rs762989436
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000422205 SCV000534992 uncertain significance not provided 2017-01-05 criteria provided, single submitter clinical testing The C20Y variant in the TTC7A gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The C20Y variant was not observed with any significant frequency in the Exome Aggregation Consortium (ExAC) data set, indicating it is not a common benign variant. The C20Y 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. In addition, this substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret C20Y as a variant of uncertain significance.
Labcorp Genetics (formerly Invitae), Labcorp RCV001851080 SCV002168982 uncertain significance Multiple gastrointestinal atresias 2022-08-16 criteria provided, single submitter clinical testing This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 20 of the TTC7A protein (p.Cys20Tyr). This variant is present in population databases (rs762989436, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with TTC7A-related conditions. ClinVar contains an entry for this variant (Variation ID: 391837). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). 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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