ClinVar Miner

Submissions for variant NM_000091.5(COL4A3):c.2489-1G>A

dbSNP: rs1574782406
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics RCV000991613 SCV001143221 likely pathogenic not provided 2018-09-21 criteria provided, single submitter clinical testing The variant disrupts a canonical splice site, and is therefore predicted to significantly disrupt the protein structure. Not found in the total gnomAD dataset, and the data is high quality (0/275976 chr).
Medical Genetics, University of Parma RCV001089907 SCV001245140 likely pathogenic Autosomal recessive Alport syndrome 2020-03-11 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000991613 SCV005781929 likely pathogenic not provided 2024-04-25 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 31 of the COL4A3 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 COL4A3 are known to be pathogenic (PMID: 8956999, 24854265, 26809805, 27281700). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with Alport syndrome (PMID: 33369211). ClinVar contains an entry for this variant (Variation ID: 804576). 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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