ClinVar Miner

Submissions for variant NM_000341.4(SLC3A1):c.1796T>C (p.Phe599Ser)

gnomAD frequency: 0.00004  dbSNP: rs146963107
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001298344 SCV001487396 uncertain significance Cystinuria 2020-02-05 criteria provided, single submitter clinical testing 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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has been observed in individuals with cystinuria (PMID: 25964309, 11748844, 28717662, 25109415). This variant is present in population databases (rs146963107, ExAC 0.007%). This sequence change replaces phenylalanine with serine at codon 599 of the SLC3A1 protein (p.Phe599Ser). The phenylalanine residue is highly conserved and there is a large physicochemical difference between phenylalanine and serine.
Fulgent Genetics, Fulgent Genetics RCV001298344 SCV005661042 likely pathogenic Cystinuria 2024-01-11 criteria provided, single submitter clinical testing

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