ClinVar Miner

Submissions for variant NM_058179.4(PSAT1):c.870-1G>T

gnomAD frequency: 0.00003  dbSNP: rs376824714
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001767372 SCV001991338 likely pathogenic not provided 2022-02-21 criteria provided, single submitter clinical testing Canonical splice site variant expected to result in aberrant splicing, although in the absence of functional evidence the actual effect of this sequence change is unknown.; This variant is associated with the following publications: (PMID: 32579715)
Labcorp Genetics (formerly Invitae), Labcorp RCV002032850 SCV002250887 pathogenic Neu-Laxova syndrome 2 2024-01-22 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 7 of the PSAT1 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 PSAT1 are known to be pathogenic (PMID: 17436247, 25152457). This variant is present in population databases (rs376824714, gnomAD 0.01%). Disruption of this splice site has been observed in individuals with clinical features of Neu-Laxova syndrome (PMID: 32579715). ClinVar contains an entry for this variant (Variation ID: 1306418). 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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