ClinVar Miner

Submissions for variant NM_001903.5(CTNNA1):c.1942T>G (p.Phe648Val)

gnomAD frequency: 0.00002  dbSNP: rs139529481
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000821462 SCV000962219 uncertain significance not provided 2024-11-11 criteria provided, single submitter clinical testing This sequence change replaces phenylalanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 648 of the CTNNA1 protein (p.Phe648Val). This variant is present in population databases (rs139529481, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with CTNNA1-related conditions. ClinVar contains an entry for this variant (Variation ID: 663564). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt CTNNA1 protein function with a negative predictive value of 80%. 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.
Ambry Genetics RCV001013795 SCV001174425 uncertain significance Hereditary cancer-predisposing syndrome 2024-06-07 criteria provided, single submitter clinical testing The p.F648V variant (also known as c.1942T>G), located in coding exon 13 of the CTNNA1 gene, results from a T to G substitution at nucleotide position 1942. The phenylalanine at codon 648 is replaced by valine, an amino acid with highly similar properties. This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. The evidence for this gene-disease relationship is limited; therefore, the clinical significance of this alteration is unclear.
GeneDx RCV000821462 SCV003926279 uncertain significance not provided 2022-11-21 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 32051609)
Baylor Genetics RCV004569763 SCV005058604 uncertain significance Patterned macular dystrophy 2 2023-11-10 criteria provided, single submitter clinical testing

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