ClinVar Miner

Submissions for variant NM_004247.4(EFTUD2):c.1058+1G>A (rs1085307647)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000488992 SCV000576932 pathogenic not provided 2017-04-14 criteria provided, single submitter clinical testing The c.1058+1G>A variant in the EFTUD2 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This splice site variant destroys the canonical splice donor site in intron 12. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. The c.1058+1G>A variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret c.1058+1G>A as a pathogenic variant.
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego RCV000853362 SCV000996230 pathogenic Mandibulofacial dysostosis-microcephaly syndrome 2018-12-28 criteria provided, single submitter clinical testing This variant affects the canonical splice donor site of intron 12 and is therefore predicted to interfere with splicing and result in loss of normal protein function. This variant has not been previously reported or functionally characterized in the literature to our knowledge. It is absent from the ExAC and gnomAD population databases and thus is presumed to be rare. Multiple splice prediction tools suggest this variant is likely to interfere with normal splicing. Based on the available evidence, the c.1058+1G>A variant is classified as pathogenic.
Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes RCV000488992 SCV001334356 pathogenic not provided 2020-02-14 criteria provided, single submitter clinical testing

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