ClinVar Miner

Submissions for variant NM_000294.3(PHKG2):c.800_801+34del

dbSNP: rs2151310413
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 2
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
3billion, Medical Genetics RCV002251200 SCV002521712 pathogenic Glycogen storage disease IXc 2022-05-22 criteria provided, single submitter clinical testing The variant is not observed in the gnomAD v2.1.1 dataset. Canonical splice site: predicted to alter splicing and result in a loss or disruption of normal protein function. Multiple pathogenic loss-of-function variants are reported downstream of the variant. Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.
Labcorp Genetics (formerly Invitae), Labcorp RCV002251200 SCV005737948 likely pathogenic Glycogen storage disease IXc 2024-04-06 criteria provided, single submitter clinical testing This variant results in the deletion of part of exon 8 (c.800_801+34del) of the PHKG2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in PHKG2 are known to be pathogenic (PMID: 8896567, 17689125, 21646031). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PHKG2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1687518). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.