ClinVar Miner

Submissions for variant NM_024642.5(GALNT12):c.1672A>G (p.Ser558Gly)

gnomAD frequency: 0.00003  dbSNP: rs759843363
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000465556 SCV000551392 uncertain significance not provided 2023-11-17 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with glycine, which is neutral and non-polar, at codon 558 of the GALNT12 protein (p.Ser558Gly). This variant is present in population databases (rs759843363, 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: 410576). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The glycine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.
Fulgent Genetics, Fulgent Genetics RCV000766033 SCV000897472 uncertain significance Colorectal cancer, susceptibility to, 1 2018-10-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV004022790 SCV001173149 uncertain significance not specified 2023-03-24 criteria provided, single submitter clinical testing The p.S558G variant (also known as c.1672A>G), located in coding exon 10 of the GALNT12 gene, results from an A to G substitution at nucleotide position 1672. The serine at codon 558 is replaced by glycine, an amino acid with similar properties. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. The evidence for this gene-disease relationship is limited; therefore, the clinical significance of this alteration is unclear.

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