ClinVar Miner

Submissions for variant NM_013296.5(GPSM2):c.1661C>A (p.Ser554Ter)

gnomAD frequency: 0.00006  dbSNP: rs145191476
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000578923 SCV000680728 pathogenic not provided 2022-05-20 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 27064331, 23494849, 22578326, 27180139, 34313030)
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center RCV000029165 SCV002061619 likely pathogenic Chudley-McCullough syndrome 2021-10-06 criteria provided, single submitter clinical testing PVS1, PM2
Invitae RCV000578923 SCV002122429 pathogenic not provided 2022-01-31 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 35493). This premature translational stop signal has been observed in individuals with Chudley-McCullough syndrome (PMID: 22578326). This variant is present in population databases (rs145191476, gnomAD 0.02%). This sequence change creates a premature translational stop signal (p.Ser554*) in the GPSM2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GPSM2 are known to be pathogenic (PMID: 22578326, 22987632).
OMIM RCV000029165 SCV000051810 pathogenic Chudley-McCullough syndrome 2012-06-08 no assertion criteria provided literature only
GenomeConnect - Invitae Patient Insights Network RCV000029165 SCV001749620 not provided Chudley-McCullough syndrome no assertion provided phenotyping only Variant interpreted as Pathogenic and reported on 06-26-2017 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.

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