ClinVar Miner

Submissions for variant NM_024642.5(GALNT12):c.1017C>A (p.Asn339Lys)

dbSNP: rs756614355
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000458771 SCV000551408 uncertain significance not provided 2022-08-09 criteria provided, single submitter clinical testing This sequence change replaces asparagine, which is neutral and polar, with lysine, which is basic and polar, at codon 339 of the GALNT12 protein (p.Asn339Lys). This variant is present in population databases (rs756614355, gnomAD 0.006%). 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: 410591). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. 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 RCV004022801 SCV001169804 uncertain significance not specified 2024-08-05 criteria provided, single submitter clinical testing The p.N339K variant (also known as c.1017C>A), located in coding exon 5 of the GALNT12 gene, results from a C to A substitution at nucleotide position 1017. The asparagine at codon 339 is replaced by lysine, an amino acid with similar properties. This amino acid position is highly 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.
Baylor Genetics RCV003470474 SCV004196140 uncertain significance Colorectal cancer, susceptibility to, 1 2023-10-11 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000458771 SCV004219743 uncertain significance not provided 2023-01-02 criteria provided, single submitter clinical testing The variant has not been reported in the published literature. The frequency of this variant in the general population, 0.000012 (3/251460 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant.
Fulgent Genetics, Fulgent Genetics RCV003470474 SCV005677643 uncertain significance Colorectal cancer, susceptibility to, 1 2024-03-13 criteria provided, single submitter clinical testing

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