ClinVar Miner

Submissions for variant NM_006772.3(SYNGAP1):c.3583-9G>A

dbSNP: rs1554122689
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000645739 SCV000767494 pathogenic Intellectual disability, autosomal dominant 5 2024-09-16 criteria provided, single submitter clinical testing This sequence change falls in intron 16 of the SYNGAP1 gene. It does not directly change the encoded amino acid sequence of the SYNGAP1 protein. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with epilepsy (internal data). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 537000). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV001731838 SCV001982169 pathogenic not provided 2022-12-08 criteria provided, single submitter clinical testing Not observed in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 30800045, 31440721)
Institute of Human Genetics, University of Leipzig Medical Center RCV000645739 SCV004242426 pathogenic Intellectual disability, autosomal dominant 5 2023-12-12 criteria provided, single submitter clinical testing Criteria applied: PVS1,PS2,PS4_MOD,PM2_SUP
GenomeConnect - Simons Searchlight RCV001265158 SCV001443193 pathogenic Complex neurodevelopmental disorder 2018-06-08 no assertion criteria provided provider interpretation Submission from Simons Searchlight facilitated by GenomeConnect. Variant interpreted by the Simons Searchlight team most recently on 2018-06-08 and interpreted as Pathogenic. Variant was initially reported on 2018-01-03 by GTR ID of laboratory name 500031. The reporting laboratory might also submit to ClinVar.
GenomeConnect, ClinGen RCV001824853 SCV002074973 not provided Intellectual disability, autosomal dominant 5; Infantile epileptic dyskinetic encephalopathy no assertion provided phenotyping only Variant interpreted as Pathogenic and reported on 01-03-2018 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

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