ClinVar Miner

Submissions for variant NM_024411.5(PDYN):c.414G>T (p.Arg138Ser)

gnomAD frequency: 0.00008  dbSNP: rs267606941
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Mendelics RCV000018094 SCV001142168 uncertain significance Spinocerebellar ataxia type 23 2023-09-29 criteria provided, single submitter clinical testing
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen RCV001268483 SCV001447446 pathogenic not provided 2020-10-23 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV001268483 SCV002064033 likely pathogenic not provided 2021-10-01 criteria provided, single submitter clinical testing
GeneDx RCV001268483 SCV002584237 uncertain significance not provided 2023-09-21 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 31589614, 21035104)
Labcorp Genetics (formerly Invitae), Labcorp RCV001268483 SCV003262120 pathogenic not provided 2024-04-15 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with serine, which is neutral and polar, at codon 138 of the PDYN protein (p.Arg138Ser). This variant is present in population databases (rs267606941, gnomAD 0.01%). This missense change has been observed in individual(s) with clinical features of spinocerebellar ataxia (PMID: 21035104, 22287014, 23355175). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 18458). 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 not expected to disrupt PDYN protein function with a negative predictive value of 80%. Studies have shown that this missense change alters PDYN gene expression (PMID: 21035104). For these reasons, this variant has been classified as Pathogenic.
Human Genetics Bochum, Ruhr University Bochum RCV000018094 SCV004042773 likely pathogenic Spinocerebellar ataxia type 23 2023-05-23 criteria provided, single submitter clinical testing ACMG criteria used to clasify this variant: PS4, PS3_MOD, PP1
OMIM RCV000018094 SCV000038373 pathogenic Spinocerebellar ataxia type 23 2010-11-12 no assertion criteria provided literature only

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