ClinVar Miner

Submissions for variant NM_006772.3(SYNGAP1):c.190-2A>G

dbSNP: rs1776941586
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001223942 SCV001396113 pathogenic Intellectual disability, autosomal dominant 5 2020-03-11 criteria provided, single submitter clinical testing Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in SYNGAP1 are known to be pathogenic (PMID: 23161826, 23708187, 26989088). For these reasons, this variant has been classified as Pathogenic. This variant has been observed in individual(s) affected with clinical features of epileptic encephalopathy (PMID: 30541864, Invitae). This sequence change affects an acceptor splice site in intron 2 of the SYNGAP1 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency).
GenomeConnect - Brain Gene Registry RCV001223942 SCV004804543 not provided Intellectual disability, autosomal dominant 5 no assertion provided phenotyping only Variant classified as Pathogenic and reported on 03-25-2016 by The Children's Hospital of Philadelphia. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Dr. Philip Payne from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/.

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