ClinVar Miner

Submissions for variant NM_000317.3(PTS):c.315-2A>G

dbSNP: rs1555198483
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000674555 SCV000799910 likely pathogenic 6-Pyruvoyl-tetrahydrobiopterin synthase deficiency 2018-05-15 criteria provided, single submitter clinical testing
Invitae RCV000674555 SCV002228227 pathogenic 6-Pyruvoyl-tetrahydrobiopterin synthase deficiency 2023-09-21 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 5 of the PTS gene. While this variant is not anticipated to result in nonsense mediated decay, it likely alters RNA splicing and results in a disrupted protein product. This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with biopterin deficient hyperphenylalanemia (PMID: 28057123, 33234470). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 558308). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). 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.
Baylor Genetics RCV000674555 SCV004207159 pathogenic 6-Pyruvoyl-tetrahydrobiopterin synthase deficiency 2023-05-31 criteria provided, single submitter clinical testing

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