ClinVar Miner

Submissions for variant NM_000030.3(AGXT):c.560C>T (p.Ser187Phe)

gnomAD frequency: 0.00002  dbSNP: rs180177238
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000128801 SCV000797737 likely pathogenic Primary hyperoxaluria, type I 2018-02-08 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003317095 SCV004020472 pathogenic Primary hyperoxaluria 2023-06-20 criteria provided, single submitter clinical testing Variant summary: AGXT c.560C>T (p.Ser187Phe) results in a non-conservative amino acid change located in the Aminotransferase class V domain (IPR000192) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-06 in 249728 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.560C>T has been reported in the literature in both compound heterozygous and homozygous individuals affected with Primary Hyperoxaluria Type 1 (e.g., Minatogawa_1992, Hoppe_1997, Hoyer-Kuhn_2014, Williams_2015), and the variant has been shown to segregate with disease in related individuals. These data indicate that the variant is likely to be associated with disease. Several publications report experimental evidence evaluating an impact on protein function, finding that the variant disrupts the enzyme active site and results in <10% of normal enzymatic activity (e.g., Oppici_2013, Coulter-Mackie_2006, Minatogawa_1992). The following publications have been ascertained in the context of this evaluation (PMID: 16971151, 9002528, 24385516, 1301173, 23589421, 25629080). One submitter has reported clinical-significance assessments for this variant to ClinVar after 2014 and has classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Baylor Genetics RCV000128801 SCV005059329 pathogenic Primary hyperoxaluria, type I 2024-02-05 criteria provided, single submitter clinical testing
GeneReviews RCV000128801 SCV000172455 not provided Primary hyperoxaluria, type I no assertion provided literature only
Clinical Biochemistry Laboratory, Health Services Laboratory RCV000128801 SCV000239655 pathogenic Primary hyperoxaluria, type I 2014-11-27 no assertion criteria provided in vitro

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