ClinVar Miner

Submissions for variant NM_024642.5(GALNT12):c.1249C>T (p.Arg417Trp)

gnomAD frequency: 0.00001  dbSNP: rs766728145
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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 RCV002033330 SCV002112249 uncertain significance not provided 2024-12-18 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 417 of the GALNT12 protein (p.Arg417Trp). This variant is present in population databases (rs766728145, gnomAD 0.02%). 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: 1348292). 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 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.
Ambry Genetics RCV004038798 SCV002668797 uncertain significance not specified 2024-04-27 criteria provided, single submitter clinical testing The p.R417W variant (also known as c.1249C>T), located in coding exon 7 of the GALNT12 gene, results from a C to T substitution at nucleotide position 1249. The arginine at codon 417 is replaced by tryptophan, 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.
Baylor Genetics RCV003464160 SCV004196137 uncertain significance Colorectal cancer, susceptibility to, 1 2023-10-12 criteria provided, single submitter clinical testing

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