ClinVar Miner

Submissions for variant NM_024642.5(GALNT12):c.1640G>C (p.Cys547Ser)

gnomAD frequency: 0.00001  dbSNP: rs368008649
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV004030341 SCV001173000 uncertain significance not specified 2023-07-26 criteria provided, single submitter clinical testing The p.C547S variant (also known as c.1640G>C), located in coding exon 10 of the GALNT12 gene, results from a G to C substitution at nucleotide position 1640. The cysteine at codon 547 is replaced by serine, an amino acid with dissimilar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Labcorp Genetics (formerly Invitae), Labcorp RCV001063457 SCV001228304 uncertain significance not provided 2024-06-18 criteria provided, single submitter clinical testing This sequence change replaces cysteine, which is neutral and slightly polar, with serine, which is neutral and polar, at codon 547 of the GALNT12 protein (p.Cys547Ser). This variant is present in population databases (rs368008649, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with GALNT12-related conditions. ClinVar contains an entry for this variant (Variation ID: 819727). 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 expected to disrupt GALNT12 protein function with a positive 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.
Baylor Genetics RCV004569901 SCV005058806 uncertain significance Colorectal cancer, susceptibility to, 1 2024-02-24 criteria provided, single submitter clinical testing

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