ClinVar Miner

Submissions for variant NM_024411.5(PDYN):c.616C>T (p.Arg206Cys)

gnomAD frequency: 0.00006  dbSNP: rs575606358
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV001091282 SCV001247216 uncertain significance not provided 2019-08-01 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001141784 SCV001302153 uncertain significance Spinocerebellar ataxia type 23 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Labcorp Genetics (formerly Invitae), Labcorp RCV001091282 SCV003290891 uncertain significance not provided 2023-12-11 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 206 of the PDYN protein (p.Arg206Cys). This variant is present in population databases (rs575606358, gnomAD 0.02%). This missense change has been observed in individual(s) with autosomal dominant cerebellar ataxia (PMID: 23471613). ClinVar contains an entry for this variant (Variation ID: 871369). 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 PDYN protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change does not substantially affect PDYN function (PMID: 23471613). This variant disrupts the p.Arg206 amino acid residue in PDYN. Other variant(s) that disrupt this residue have been observed in individuals with PDYN-related conditions (PMID: 23471613), which suggests that this may be a clinically significant amino acid residue. 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.

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