ClinVar Miner

Submissions for variant NM_017837.4(PIGV):c.146C>A (p.Ser49Ter)

gnomAD frequency: 0.00003  dbSNP: rs145160045
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV002274770 SCV002559723 pathogenic not provided 2023-08-15 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 significant frequency in large population cohorts (gnomAD); Has not been previously reported as pathogenic or benign in association with neurodevelopmental disorders to our knowledge; This variant is associated with the following publications: (PMID: 31345219)
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center RCV003387542 SCV004099144 pathogenic Hyperphosphatasia with intellectual disability syndrome 1 2023-09-15 criteria provided, single submitter clinical testing PVS1, PM2, PM3
PreventionGenetics, part of Exact Sciences RCV004529114 SCV004104760 uncertain significance PIGV-related disorder 2022-10-25 criteria provided, single submitter clinical testing The PIGV c.146C>A variant is predicted to result in premature protein termination (p.Ser49*). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0031% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-27120671-C-A). Loss of function has not been an established mechanism for PIGV-related disease and the majority of reported pathogenic variants have been missense variants. Although we suspect that this variant may be pathogenic, at this time, its clinical significance is uncertain due to the absence of conclusive functional and genetic information.

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