ClinVar Miner

Submissions for variant NM_015599.3(PGM3):c.1474C>T (p.Arg492Ter) (rs144104577)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000613688 SCV000713007 likely pathogenic Immunodeficiency 23 2017-04-06 criteria provided, single submitter clinical testing The p.Arg520X variant in PGM3 has not been previously reported in individuals wi th immunodeficiency, but has been identified in 4/66736 European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs 144104577). This nonsense variant leads to a premature termination codon at posi tion 520, which is predicted to lead to a truncated or absent protein. Bialleli c variants in the PGM3 gene that result in reduced PGM3 expression and/or enzyma tic function are reported to cause autosomal recessive immunodeficiency 23 (MIM: 615816). In summary, although additional studies are required to fully establi sh its clinical significance, the p.Arg520X variant is likely pathogenic.
Invitae RCV000613688 SCV000933408 pathogenic Immunodeficiency 23 2018-12-18 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg520*) in the PGM3 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs144104577, ExAC 0.006%). This variant has not been reported in the literature in individuals with PGM3-related conditions. ClinVar contains an entry for this variant (Variation ID: 505650). Loss-of-function variants in PGM3 are known to be pathogenic (PMID: 17548465, 24589341, 24931394). For these reasons, this variant has been classified as Pathogenic.

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