ClinVar Miner

Submissions for variant NM_024854.5(PYROXD1):c.365G>A (p.Cys122Tyr)

gnomAD frequency: 0.00129  dbSNP: rs140460108
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001787567 SCV002031001 likely benign not provided 2021-05-05 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001787567 SCV002298148 uncertain significance not provided 2022-11-01 criteria provided, single submitter clinical testing This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 122 of the PYROXD1 protein (p.Cys122Tyr). This variant is present in population databases (rs140460108, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with PYROXD1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1327287). 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 PYROXD1 protein function. 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 RCV002544311 SCV003754806 uncertain significance Inborn genetic diseases 2021-10-06 criteria provided, single submitter clinical testing The c.365G>A (p.C122Y) alteration is located in exon 4 (coding exon 4) of the PYROXD1 gene. This alteration results from a G to A substitution at nucleotide position 365, causing the cysteine (C) at amino acid position 122 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
CeGaT Center for Human Genetics Tuebingen RCV001787567 SCV005891144 likely benign not provided 2025-02-01 criteria provided, single submitter clinical testing PYROXD1: BP4, BS2

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