ClinVar Miner

Submissions for variant NM_006772.3(SYNGAP1):c.427C>T (p.Arg143Ter)

dbSNP: rs397514741
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000054513 SCV000249104 pathogenic Intellectual disability, autosomal dominant 5 2015-01-05 criteria provided, single submitter clinical testing
GeneDx RCV000599367 SCV000709920 pathogenic not provided 2023-06-23 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: 23708187, 30541864, 31395010, 33144682, 31440721)
Labcorp Genetics (formerly Invitae), Labcorp RCV000054513 SCV000767491 pathogenic Intellectual disability, autosomal dominant 5 2023-11-27 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg143*) in the SYNGAP1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SYNGAP1 are known to be pathogenic (PMID: 23161826, 23708187, 26989088). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with SYNGAP1-related conditions (PMID: 23708187, 30541864). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 60716). For these reasons, this variant has been classified as Pathogenic.
Fulgent Genetics, Fulgent Genetics RCV000054513 SCV000893715 pathogenic Intellectual disability, autosomal dominant 5 2018-10-31 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000599367 SCV001248667 pathogenic not provided 2023-02-01 criteria provided, single submitter clinical testing SYNGAP1: PS2:Very Strong, PVS1, PM2, PS4:Moderate
Génétique des Maladies du Développement, Hospices Civils de Lyon RCV000054513 SCV001250625 pathogenic Intellectual disability, autosomal dominant 5 criteria provided, single submitter clinical testing
Institute of Human Genetics, University of Leipzig Medical Center RCV000054513 SCV002044440 pathogenic Intellectual disability, autosomal dominant 5 2021-12-10 criteria provided, single submitter clinical testing This variant was identified as de novo (maternity and paternity confirmed)._x000D_ Criteria applied: PVS1, PS2, PS4_MOD, PM2_SUP
Department of Clinical Genetics, Medical University of Lodz RCV000054513 SCV004801755 pathogenic Intellectual disability, autosomal dominant 5 2023-07-27 criteria provided, single submitter literature only
OMIM RCV000054513 SCV000082991 pathogenic Intellectual disability, autosomal dominant 5 2013-07-01 no assertion criteria provided literature only
GenomeConnect - Simons Searchlight RCV001265523 SCV001443667 pathogenic Complex neurodevelopmental disorder 2018-04-16 no assertion criteria provided provider interpretation Submission from Simons Searchlight facilitated by GenomeConnect. Variant interpreted by the Simons Searchlight team most recently on 2018-04-16 and interpreted as Pathogenic. Variant was initially reported on 2017-10-09 by GTR ID of laboratory name 500031. The reporting laboratory might also submit to ClinVar.

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