ClinVar Miner

Submissions for variant NM_152594.3(SPRED1):c.304dup (p.Thr102fs)

gnomAD frequency: 0.00001  dbSNP: rs1555391053
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000645296 SCV000767039 pathogenic Legius syndrome 2023-04-06 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 536688). This premature translational stop signal has been observed in individual(s) with Legius syndrome (PMID: 21089071). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Thr102Asnfs*7) in the SPRED1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SPRED1 are known to be pathogenic (PMID: 17704776).
Center for Human Genetics, Inc, Center for Human Genetics, Inc RCV000645296 SCV000782324 pathogenic Legius syndrome 2016-11-01 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV001813534 SCV002060949 pathogenic Noonan syndrome and Noonan-related syndrome 2020-09-25 criteria provided, single submitter clinical testing
GeneDx RCV003318616 SCV004022812 pathogenic not provided 2023-07-27 criteria provided, single submitter clinical testing Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 17704776, 21548021, 27322474, 22753041, 28747691, 21089071)

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