ClinVar Miner

Submissions for variant NM_004586.3(RPS6KA3):c.1603-5A>G

dbSNP: rs1569194162
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000702364 SCV000831216 likely pathogenic Coffin-Lowry syndrome; Intellectual disability, X-linked 19 2021-10-11 criteria provided, single submitter clinical testing This variant has been observed in individuals with clinical features of Coffin Lowry syndrome (PMID: 16306095; Invitae). This variant is not present in population databases (ExAC no frequency). This sequence change falls in intron 17 of the RPS6KA3 gene. It does not directly change the encoded amino acid sequence of the RPS6KA3 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. ClinVar contains an entry for this variant (Variation ID: 579151). 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. Studies have shown that this variant results in altered splicing, which introduces a premature termination codon (PMID: 16306095). The resulting mRNA is expected to undergo nonsense-mediated decay.
Revvity Omics, Revvity RCV001784342 SCV002019077 likely pathogenic not provided 2020-06-04 criteria provided, single submitter clinical testing
GeneDx RCV001784342 SCV002498852 uncertain significance not provided 2022-03-17 criteria provided, single submitter clinical testing Reported previously in individuals with Coffin-Lowry syndrome, however additional clinical information was not provided (Falco et al., 2005); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 16306095)

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