ClinVar Miner

Submissions for variant NM_000030.3(AGXT):c.525-1G>A

gnomAD frequency: 0.00001  dbSNP: rs180177234
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000186372 SCV000799315 pathogenic Primary hyperoxaluria, type I 2018-04-09 criteria provided, single submitter clinical testing
Invitae RCV001852427 SCV002238433 pathogenic not provided 2023-10-14 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 4 of the AGXT 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 AGXT are known to be pathogenic (PMID: 19479957). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with primary hyperoxaluria type 1 (PMID: 10862087, 17460142). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as 647-1G>A. ClinVar contains an entry for this variant (Variation ID: 204165). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Clinical Biochemistry Laboratory, Health Services Laboratory RCV000186372 SCV000239719 pathogenic Primary hyperoxaluria, type I 2014-11-27 no assertion criteria provided research

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