ClinVar Miner

Submissions for variant NM_000030.3(AGXT):c.32C>T (p.Pro11Leu) (rs34116584)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000173049 SCV000224129 benign not specified 2014-09-24 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000173049 SCV000301569 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000290977 SCV000429355 likely benign Primary hyperoxaluria 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000587789 SCV000693978 likely benign not provided 2017-06-26 criteria provided, single submitter clinical testing Variant summary: The AGXT c.32C>T (p.Pro11Leu) variant involves the alteration of a conserved nucleotide and is predicted to be damaging by 3/3 in silico tools. This variant was found in 17684/114424 control chromosomes (1706 homozygotes) (including ExAC) at a frequency of 0.154548, which is approximately 65 times the estimated maximal expected allele frequency of a pathogenic AGXT variant (0.0023717), thus this variant is common polymorphism. Available clinical and functional data show that this variant leads to synergistic effect with some common pathogenic variants (such as Gly170Arg and p.Ile244Thr) and presence of this variant in the same chromosome (in cis) with those pathogenic variants is required for their loss of function effect (Lumb_2000, Santana_2003, Van Woerden_2004, Lorenzo_2006, Monico_2007, Kanoun_2013). Multiple clinical diagnostic laboratories/reputable databases have classified this variant as benign/likely benign. Taken together, primarily based on its role as a functional polymorphism and fact that its presence is required for determining pathogenicity of other mutations, this variant is classified as likely benign.
OMIM RCV000005995 SCV000026177 benign Primary hyperoxaluria, type I 2013-01-25 no assertion criteria provided literature only
GeneReviews RCV000005995 SCV000172447 benign Primary hyperoxaluria, type I 2014-07-17 no assertion criteria provided literature only
Clinical Biochemistry Laboratory,Health Services Laboratory RCV000005995 SCV000239543 uncertain significance Primary hyperoxaluria, type I 2014-11-27 no assertion criteria provided in vitro

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