ClinVar Miner

Submissions for variant NM_000151.4(G6PC1):c.980_982del (p.Phe327del)

dbSNP: rs80356486
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000409898 SCV000486957 likely pathogenic Glycogen storage disease due to glucose-6-phosphatase deficiency type IA 2016-09-14 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000409898 SCV001338491 pathogenic Glycogen storage disease due to glucose-6-phosphatase deficiency type IA 2020-04-02 criteria provided, single submitter clinical testing Variant summary: G6PC c.980_982delTCT (p.Phe327del) results in an in-frame deletion that is predicted to remove one amino acid from the encoded protein. The variant allele was found at a frequency of 4e-06 in 251410 control chromosomes (gnomAD). c.980_982delTCT (p.Phe327del) has been reported in the literature in multiple individuals (both homozygous and compound heterozygous) affected with Glycogen Storage Disease Type Ia (e.g. Lei_1995, Kishnani_2009). These data indicate that the variant is very likely to be associated with disease. In functional studies, the variant was found to have very low or no enzymatic activity (e.g. Lei_1995, Shieh_2002). Two ClinVar submitters (evaluation after 2014) cite the variant as likely pathogenic/pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Invitae RCV000409898 SCV002510574 pathogenic Glycogen storage disease due to glucose-6-phosphatase deficiency type IA 2021-11-18 criteria provided, single submitter clinical testing This variant, c.980_982del, results in the deletion of 1 amino acid(s) of the G6PC protein (p.Phe327del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs770928376, gnomAD 0.002%). This variant has been observed in individual(s) with glycogen storage disease (PMID: 7814621, 10834516, 11739393). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as c.1057delTTC or delta F327. ClinVar contains an entry for this variant (Variation ID: 371388). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects G6PC function (PMID: 7814621, 11739393). For these reasons, this variant has been classified as Pathogenic.
National Center for Biotechnology Information, National Institutes of Health RCV000409898 SCV000298098 pathogenic Glycogen storage disease due to glucose-6-phosphatase deficiency type IA 2016-08-25 no assertion criteria provided literature only
Natera, Inc. RCV000409898 SCV002093332 pathogenic Glycogen storage disease due to glucose-6-phosphatase deficiency type IA 2017-03-17 no assertion criteria provided clinical testing

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