ClinVar Miner

Submissions for variant NM_058179.4(PSAT1):c.949G>T (p.Glu317Ter)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002953061 SCV003273399 pathogenic Neu-Laxova syndrome 2 2024-11-11 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Glu317*) in the PSAT1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PSAT1 are known to be pathogenic (PMID: 17436247, 25152457). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PSAT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 2061942). 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003230758 SCV003928646 likely pathogenic PSAT1-related disorder 2023-04-20 criteria provided, single submitter clinical testing Variant summary: PSAT1 c.949G>T (p.Glu317X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant was absent in 251152 control chromosomes. To our knowledge, no occurrence of c.949G>T in individuals affected with PSAT1-Related Disorders and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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