ClinVar Miner

Submissions for variant NM_015599.3(PGM3):c.-2-194C>T

gnomAD frequency: 0.00003  dbSNP: rs753019951
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001388396 SCV001589367 pathogenic Immunodeficiency 23 2024-10-16 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Gln21*) in the PGM3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PGM3 are known to be pathogenic (PMID: 17548465, 24589341, 24931394). This variant is present in population databases (rs753019951, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with PGM3-related conditions. ClinVar contains an entry for this variant (Variation ID: 1074940). For these reasons, this variant has been classified as Pathogenic.
Revvity Omics, Revvity RCV001388396 SCV002024592 likely pathogenic Immunodeficiency 23 2021-08-25 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV001820088 SCV002065825 likely pathogenic not provided 2021-11-23 criteria provided, single submitter clinical testing DNA sequence analysis of the PGM gene demonstrated a sequence change, c.61C>T, which results in the creation of a premature stop codon at amino acid position 21, p.Gln21*. This likely pathogenic sequence change is predicted to result in an abnormal transcript, which may be degraded, or may lead to the production of a truncated PGM protein with potentially abnormal function. This sequence change has been described in the gnomAD database with a frequency of 0.012% in the Ashkenazi Jewish subpopulation (dbSNP rs753019951). This likely pathogenic sequence change has not previously been described in an individual with PGM-related disorders, however other downstream truncating variants in the PGM gene have been reported in association with disease. Loss-of-function variants in PGM3 are known to be pathogenic(PMID: 17548465, 24589341, 24931394).
AiLife Diagnostics, AiLife Diagnostics RCV001820088 SCV002502624 likely pathogenic not provided 2022-03-23 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003405636 SCV004107106 uncertain significance PGM3-related disorder 2023-08-24 criteria provided, single submitter clinical testing The PGM3 c.61C>T variant is predicted to result in premature protein termination (p.Gln21*). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.012% of alleles in individuals of Ashkenazi Jewish descent in gnomAD (http://gnomad.broadinstitute.org/variant/6-83900927-G-A) and has interpretations of Pathogenic/Likely Pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/1074940/). Of note, this variant is present in an exon which is spliced out of the primary PGM3 transcript. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Fulgent Genetics, Fulgent Genetics RCV001388396 SCV005674031 likely pathogenic Immunodeficiency 23 2024-04-02 criteria provided, single submitter clinical testing

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