ClinVar Miner

Submissions for variant NM_020461.4(TUBGCP6):c.5389C>T (p.Arg1797Cys)

gnomAD frequency: 0.00004  dbSNP: rs138609686
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000413552 SCV000491896 uncertain significance not provided 2016-11-11 criteria provided, single submitter clinical testing The R1797C variant in the TUBGCP6 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The R1797C variant was not observed at any significant frequency in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The R1797C 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 across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret R1797C as a variant of uncertain significance.
Invitae RCV000413552 SCV001389246 uncertain significance not provided 2022-08-07 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 1797 of the TUBGCP6 protein (p.Arg1797Cys). This variant is present in population databases (rs138609686, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with TUBGCP6-related conditions. ClinVar contains an entry for this variant (Variation ID: 373311). 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: "Probably Damaging"; 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.
Baylor Genetics RCV001329757 SCV001521282 uncertain significance Microcephaly and chorioretinopathy 1 2019-08-08 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].

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