ClinVar Miner

Submissions for variant NM_014053.4(FLVCR1):c.847G>C (p.Ala283Pro)

gnomAD frequency: 0.00003  dbSNP: rs777525949
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000522232 SCV000619189 pathogenic not provided 2024-11-15 criteria provided, single submitter clinical testing Published functional studies demonstrate a damaging effect with reduced choline transport activity (PMID: 38055060); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 37734845, 28559085, 32531858, 30656474, 37469134, 38055060)
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen RCV000522232 SCV001446626 likely pathogenic not provided 2020-10-23 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000522232 SCV003459780 likely pathogenic not provided 2022-02-19 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 283 of the FLVCR1 protein (p.Ala283Pro). This variant is present in population databases (rs777525949, gnomAD 0.002%). This missense change has been observed in individual(s) with clinical features of FLVCR1-related conditions (PMID: 28559085, 30656474; Invitae). 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: 450589). 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: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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.

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