ClinVar Miner

Submissions for variant NM_004482.4(GALNT3):c.1681T>A (p.Cys561Ser)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV003665467 SCV004374760 likely pathogenic not provided 2024-07-19 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 561 of the GALNT3 protein (p.Cys561Ser). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with tumoral calcinosis (PMID: 33614378). It has also been observed to segregate with disease in related individuals. 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 GALNT3 protein function with a positive predictive value of 80%. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Fulgent Genetics, Fulgent Genetics RCV005030142 SCV005652090 likely pathogenic Tumoral calcinosis, hyperphosphatemic, familial, 1 2024-03-21 criteria provided, single submitter clinical testing

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