ClinVar Miner

Submissions for variant NM_000317.3(PTS):c.243_243+1dup

gnomAD frequency: 0.00003  dbSNP: rs866922524
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000669844 SCV000794636 likely pathogenic 6-Pyruvoyl-tetrahydrobiopterin synthase deficiency 2017-10-09 criteria provided, single submitter clinical testing
Invitae RCV000669844 SCV000955904 likely pathogenic 6-Pyruvoyl-tetrahydrobiopterin synthase deficiency 2023-12-26 criteria provided, single submitter clinical testing This sequence change affects a splice site in intron 4 of the PTS 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 PTS are known to be pathogenic (PMID: 3297709, 16917893). This variant is present in population databases (no rsID available, gnomAD 0.002%). Disruption of this splice site has been observed in individual(s) with biopterin deficient hyperphenylalanemia (PMID: 32651154). ClinVar contains an entry for this variant (Variation ID: 554248). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Baylor Genetics RCV000669844 SCV004207147 likely pathogenic 6-Pyruvoyl-tetrahydrobiopterin synthase deficiency 2023-08-30 criteria provided, single submitter clinical testing

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