ClinVar Miner

Submissions for variant NM_015599.3(PGM3):c.162del (p.Lys54fs)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003487265 SCV004242020 pathogenic Severe combined immunodeficiency disease 2023-12-08 criteria provided, single submitter clinical testing Variant summary: PGM3 c.246delA (p.Lys82AsnfsX4) results in a premature termination codon and is expected to cause absence of the protein due to nonsense mediated decay, a commonly known mechanism for disease. The variant was absent in 251492 control chromosomes (gnomAD). To our knowledge, no occurrence of c.246delA in individuals affected with Severe Combined Immunodeficiency and no experimental evidence demonstrating its impact on protein function have been reported. No submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV003779286 SCV004652123 pathogenic Immunodeficiency 23 2023-12-30 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Lys82Asnfs*4) 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). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with PGM3-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

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