ClinVar Miner

Submissions for variant NM_022445.4(TPK1):c.92A>C (p.Tyr31Ser)

gnomAD frequency: 0.00002  dbSNP: rs531486319
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000801466 SCV000941243 uncertain significance Childhood encephalopathy due to thiamine pyrophosphokinase deficiency 2021-04-20 criteria provided, single submitter clinical testing This sequence change replaces tyrosine with serine at codon 31 of the TPK1 protein (p.Tyr31Ser). The tyrosine residue is weakly conserved and there is a large physicochemical difference between tyrosine and serine. This variant is present in population databases (rs531486319, ExAC 0.1%). This variant has not been reported in the literature in individuals with TPK1-related conditions. 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 serine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Baylor Genetics RCV000801466 SCV001520669 uncertain significance Childhood encephalopathy due to thiamine pyrophosphokinase deficiency 2020-03-12 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
GeneDx RCV005241406 SCV005888923 uncertain significance not provided 2024-09-13 criteria provided, single submitter clinical testing In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

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