ClinVar Miner

Submissions for variant NM_000642.3(AGL):c.1759C>T (p.His587Tyr) (rs139488862)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000335847 SCV000346071 uncertain significance Glycogen storage disease type III 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000506919 SCV000602454 uncertain significance none provided 2020-02-03 criteria provided, single submitter clinical testing The p.His587Tyr variant (rs139488862) has not been reported in the medical literature; however, it is listed in the ClinVar database as a variant of uncertain significance (Variation ID: 291333). It is listed in the NHLBI GO Exome Sequencing Project (ESP) with an overall allele frequency of 0.05% (identified in 6 out of 13,006 chromosomes), and in the Exome Aggregation Consortium (ExAC) browser with an overall frequency of 0.05% (identified in 59 out of 121,372 chromosomes). The histidine at codon 587 is moderately conserved considering 12 species (Alamut software v2.8.1), and computational analyses suggest this variant has a significant effect on AGL protein structure/function (SIFT: damaging, PolyPhen2: probably damaging, and Mutation Taster: disease causing). However, based on the available information, the clinical significance of the p.His587Tyr variant cannot be determined with certainty.
Invitae RCV000335847 SCV000626678 benign Glycogen storage disease type III 2020-11-15 criteria provided, single submitter clinical testing
GeneDx RCV001567373 SCV001791041 uncertain significance not provided 2021-03-18 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
CeGaT Praxis fuer Humangenetik Tuebingen RCV001567373 SCV001961127 uncertain significance not provided 2021-07-01 criteria provided, single submitter clinical testing
Natera, Inc. RCV000335847 SCV001457974 likely benign Glycogen storage disease type III 2019-11-22 no assertion criteria provided clinical testing

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