ClinVar Miner

Submissions for variant NM_004586.3(RPS6KA3):c.1894C>T (p.Arg632Ter) (rs1085307639)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000489984 SCV000576914 pathogenic not provided 2018-11-16 criteria provided, single submitter clinical testing TThe R632X nonsense variant in the RPS6KA3 gene has been reported previously in an individual with Coffin-Lowry syndrome (Aref-Eshghi et al., 2018). This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The R632X variant is not observed in large population cohorts (Lek et al., 2016). Therefore, R632X is considered a pathogenic variant.
Institute for Genomic Medicine (IGM) Clinical Laboratory,Nationwide Children's Hospital RCV001249648 SCV001423707 pathogenic Coffin-Lowry syndrome 2017-10-16 criteria provided, single submitter clinical testing [ACMG/AMP: PVS1, PS2, PM2, PP5] This alteration is a null variant in a gene where LOF is a known mechanism of disease [PVS1], is de novo in origin as it was not detected in the submitted parental specimens (identity confirmed) [PS2], is absent from or rarely observed in large-scale population databases [PM2], was reported as a pathogenic/likely pathogenic alteration by a reputable source (ClinVar or other correspondence from a clinical testing laboratory) [PP5].

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