ClinVar Miner

Submissions for variant NM_000289.6(PFKM):c.115C>T (p.Arg39Ter)

dbSNP: rs1064795749
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000485301 SCV000571858 likely pathogenic not provided 2016-10-06 criteria provided, single submitter clinical testing The R39X likely pathogenic variant in the PFKM gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The R39X variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The R39X variant is a strong candidate for a pathogenic variant, however the possibility it may be a rare benign variant cannot be excluded.
Invitae RCV001274001 SCV002229517 pathogenic Glycogen storage disease, type VII 2022-04-15 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg39*) in the PFKM gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PFKM are known to be pathogenic (PMID: 7825568, 8037209). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PFKM-related conditions. ClinVar contains an entry for this variant (Variation ID: 422391). For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV001274001 SCV004203962 likely pathogenic Glycogen storage disease, type VII 2022-07-09 criteria provided, single submitter clinical testing
Natera, Inc. RCV001274001 SCV001457675 likely pathogenic Glycogen storage disease, type VII 2020-09-16 no assertion criteria provided clinical testing

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