ClinVar Miner

Submissions for variant NM_052859.4(RFT1):c.1325G>A (p.Arg442Gln)

gnomAD frequency: 0.00002  dbSNP: rs749968109
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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 RCV000190251 SCV004616383 likely pathogenic RFT1-congenital disorder of glycosylation 2024-11-15 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 442 of the RFT1 protein (p.Arg442Gln). This variant is present in population databases (rs749968109, gnomAD 0.006%). This missense change has been observed in individual(s) with clinical features of RFT1-congenital disorder of glycosylation (PMID: 23111317, 26892341). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 207991). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt RFT1 protein function with a positive predictive value of 80%. 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.
Juno Genomics, Hangzhou Juno Genomics, Inc RCV000190251 SCV005416528 likely pathogenic RFT1-congenital disorder of glycosylation criteria provided, single submitter clinical testing PM2_Supporting+PP3_Strong+PM3_Supporting+PP4
OMIM RCV000190251 SCV000243775 pathogenic RFT1-congenital disorder of glycosylation 2012-12-01 no assertion criteria provided literature only

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