ClinVar Miner

Submissions for variant NM_000151.4(G6PC1):c.508C>T (p.Arg170Ter) (rs373345919)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genome Diagnostics Laboratory,University Medical Center Utrecht RCV000624988 SCV000743369 pathogenic Glycogen storage disease due to glucose-6-phosphatase deficiency type IA 2015-12-09 criteria provided, single submitter clinical testing
Invitae RCV000624988 SCV000823732 pathogenic Glycogen storage disease due to glucose-6-phosphatase deficiency type IA 2020-01-04 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg170*) in the G6PC gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs373345919, ExAC 0.004%). This variant has been reported in the homozygous or compound heterozygous state in individuals affected with glycogen storage disease type 1a (PMID: 15455297, 10797430, 10094563). ClinVar contains an entry for this variant (Variation ID: 522204). Loss-of-function variants in G6PC are known to be pathogenic (PMID: 8182131). For these reasons, this variant has been classified as Pathogenic.
Fulgent Genetics,Fulgent Genetics RCV000624988 SCV000894122 pathogenic Glycogen storage disease due to glucose-6-phosphatase deficiency type IA 2018-10-31 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000624988 SCV000917380 pathogenic Glycogen storage disease due to glucose-6-phosphatase deficiency type IA 2018-02-26 criteria provided, single submitter clinical testing Variant summary: G6PC c.508C>T (p.Arg170X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory (eg. c.1039C>T, p.Gln347X). Two of two in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2.5e-05 in 121412 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in G6PC causing Glycogen Storage Disease Type Ia (2.5e-05 vs 0.0017), allowing no conclusion about variant significance. c.508C>T has been reported in the literature in multiple individuals affected with Glycogen Storage Disease Type Ia. These data indicate that the variant is very likely to be associated with disease. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as pathogenic.
Mendelics RCV000624988 SCV001140452 pathogenic Glycogen storage disease due to glucose-6-phosphatase deficiency type IA 2019-05-28 criteria provided, single submitter clinical testing
Baylor Genetics RCV000624988 SCV001163784 pathogenic Glycogen storage disease due to glucose-6-phosphatase deficiency type IA criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000624988 SCV000745678 pathogenic Glycogen storage disease due to glucose-6-phosphatase deficiency type IA 2017-05-19 no assertion criteria provided clinical testing

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