ClinVar Miner

Submissions for variant NM_032634.4(PIGO):c.2855-3C>T

gnomAD frequency: 0.00001  dbSNP: rs746026821
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001768896 SCV001993660 uncertain significance not provided 2019-05-09 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); Has not been previously published as pathogenic or benign to our knowledge; In-silico analysis, which includes splice predictors and evolutionary conservation, is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.
Labcorp Genetics (formerly Invitae), Labcorp RCV002540258 SCV003297087 uncertain significance Hyperphosphatasia with intellectual disability syndrome 2 2022-08-13 criteria provided, single submitter clinical testing In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. ClinVar contains an entry for this variant (Variation ID: 1305689). This variant has not been reported in the literature in individuals affected with PIGO-related conditions. This variant is present in population databases (rs746026821, gnomAD 0.003%). This sequence change falls in intron 8 of the PIGO gene. It does not directly change the encoded amino acid sequence of the PIGO protein. It affects a nucleotide within the consensus splice site.

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