ClinVar Miner

Submissions for variant NM_004655.4(AXIN2):c.428G>A (p.Ser143Asn)

gnomAD frequency: 0.00002  dbSNP: rs761849564
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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 RCV000473887 SCV000548639 uncertain significance Oligodontia-cancer predisposition syndrome 2023-12-25 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 143 of the AXIN2 protein (p.Ser143Asn). This variant is present in population databases (rs761849564, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with AXIN2-related conditions. ClinVar contains an entry for this variant (Variation ID: 408831). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt AXIN2 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.
Sema4, Sema4 RCV002257722 SCV002537196 uncertain significance Hereditary cancer-predisposing syndrome 2021-12-16 criteria provided, single submitter curation
Ambry Genetics RCV002257722 SCV002629559 benign Hereditary cancer-predisposing syndrome 2024-03-11 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Baylor Genetics RCV003476077 SCV004212994 uncertain significance Colorectal cancer 2023-10-15 criteria provided, single submitter clinical testing

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