ClinVar Miner

Submissions for variant NM_000278.5(PAX2):c.616+6G>C

gnomAD frequency: 0.00009  dbSNP: rs180903301
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001067057 SCV001232089 uncertain significance Renal coloboma syndrome; Focal segmental glomerulosclerosis 7 2025-01-15 criteria provided, single submitter clinical testing This sequence change falls in intron 5 of the PAX2 gene. It does not directly change the encoded amino acid sequence of the PAX2 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs180903301, gnomAD 0.05%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with PAX2-related conditions. ClinVar contains an entry for this variant (Variation ID: 860696). 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. 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.
GeneDx RCV001759839 SCV001996726 uncertain significance not provided 2019-10-29 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; In silico analysis, which includes splice predictors and evolutionary conservation, supports that this variant does not alter protein structure/function

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