ClinVar Miner

Submissions for variant NM_153006.3(NAGS):c.1097-2A>G

dbSNP: rs2049106256
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001246639 SCV001420011 pathogenic Hyperammonemia, type III 2023-06-02 criteria provided, single submitter clinical testing ClinVar contains an entry for this variant (Variation ID: 970970). Disruption of this splice site has been observed in individual(s) with N-acetylglutamate synthase deficiency (PMID: 15714518, 27570737). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 4 of the NAGS 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 NAGS are known to be pathogenic (PMID: 12594532). For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site.
Baylor Genetics RCV001246639 SCV004199450 likely pathogenic Hyperammonemia, type III 2023-09-05 criteria provided, single submitter clinical testing
Natera, Inc. RCV001246639 SCV002093347 likely pathogenic Hyperammonemia, type III 2020-09-14 no assertion criteria provided clinical testing

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