ClinVar Miner

Submissions for variant NM_000317.3(PTS):c.166G>A (p.Val56Met)

dbSNP: rs104894277
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000000510 SCV000791881 likely pathogenic 6-Pyruvoyl-tetrahydrobiopterin synthase deficiency 2017-05-30 criteria provided, single submitter clinical testing
Invitae RCV000000510 SCV000957583 pathogenic 6-Pyruvoyl-tetrahydrobiopterin synthase deficiency 2021-11-30 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 56 of the PTS protein (p.Val56Met). This variant is present in population databases (rs104894277, gnomAD 0.02%). This missense change has been observed in individual(s) with biopterin-deficient hyperphenylalaninemia (PMID: 9450907, 23138986). ClinVar contains an entry for this variant (Variation ID: 481). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The methionine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. For these reasons, this variant has been classified as Pathogenic.
Genome-Nilou Lab RCV000000510 SCV002014501 pathogenic 6-Pyruvoyl-tetrahydrobiopterin synthase deficiency 2021-09-05 criteria provided, single submitter clinical testing
OMIM RCV000000510 SCV000020659 pathogenic 6-Pyruvoyl-tetrahydrobiopterin synthase deficiency 1998-01-01 no assertion criteria provided literature only
Natera, Inc. RCV000000510 SCV001452592 pathogenic 6-Pyruvoyl-tetrahydrobiopterin synthase deficiency 2020-09-16 no assertion criteria provided clinical testing

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