ClinVar Miner

Submissions for variant NM_015937.6(PIGT):c.188-2A>G

gnomAD frequency: 0.00002  dbSNP: rs771691280
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000481407 SCV000569947 likely pathogenic not provided 2022-12-23 criteria provided, single submitter clinical testing Canonical splice site variant predicted to result in a null allele 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 published as pathogenic or benign to our knowledge
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden RCV000481407 SCV002011620 pathogenic not provided 2021-11-03 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001770371 SCV002280617 likely pathogenic Multiple congenital anomalies-hypotonia-seizures syndrome 3 2024-10-15 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 1 of the PIGT gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in PIGT are known to be pathogenic (PMID: 24906948, 25943031). This variant is present in population databases (rs771691280, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with PIGT-related conditions. ClinVar contains an entry for this variant (Variation ID: 420919). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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.

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