ClinVar Miner

Submissions for variant NM_015559.3(SETBP1):c.1876C>T (p.Arg626Ter)

dbSNP: rs606231273
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000333880 SCV000329813 pathogenic not provided 2023-10-10 criteria provided, single submitter clinical testing Nonsense 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: 34490615, 33907317, 25217958)
Fulgent Genetics, Fulgent Genetics RCV000763028 SCV000893495 pathogenic Schinzel-Giedion syndrome; Intellectual disability, autosomal dominant 29 2018-10-31 criteria provided, single submitter clinical testing
Invitae RCV000333880 SCV004297831 pathogenic not provided 2023-05-16 criteria provided, single submitter clinical testing This premature translational stop signal has been observed in individual(s) with clinical features of SETBP1-related conditions (PMID: 25217958, 33907317, 34490615). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 157560). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Arg626*) in the SETBP1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SETBP1 are known to be pathogenic (PMID: 21037274, 25217958).
PreventionGenetics, part of Exact Sciences RCV003895019 SCV004710303 pathogenic SETBP1-related condition 2023-12-06 criteria provided, single submitter clinical testing The SETBP1 c.1876C>T variant is predicted to result in premature protein termination (p.Arg626*). This variant was reported in an individual with neurodevelopmental disorder (Coe. 2014. PubMed ID: 25217958; Morgan. 2021. PubMed ID: 33907317; van der Ven. 2021. PubMed ID: 34490615). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Nonsense variants in SETBP1 are expected to be pathogenic. This variant is interpreted as pathogenic.
OMIM RCV000144905 SCV000191907 pathogenic Intellectual disability, autosomal dominant 29 2014-10-01 no assertion criteria provided literature only
GenomeConnect - Simons Searchlight RCV000144905 SCV001443459 pathogenic Intellectual disability, autosomal dominant 29 2018-04-06 no assertion criteria provided provider interpretation Submission from Simons Searchlight facilitated by GenomeConnect. Variant interpreted by the Simons Searchlight team most recently on 2018-04-06 and interpreted as Pathogenic. Variant was initially reported on 2017-06-20 by GTR ID of laboratory name Radbound UMC . The reporting laboratory might also submit to ClinVar.

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