ClinVar Miner

Submissions for variant NM_006772.3(SYNGAP1):c.3233_3236del (p.Val1078fs)

dbSNP: rs1554122341
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000645731 SCV000767484 pathogenic Intellectual disability, autosomal dominant 5 2020-06-12 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in SYNGAP1 are known to be pathogenic (PMID: 23161826, 23708187, 26989088). This variant has been observed in individual(s) with SYNGAP1-related conditions (PMID: 31395010). ClinVar contains an entry for this variant (Variation ID: 536991). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Val1078Alafs*51) in the SYNGAP1 gene. It is expected to result in an absent or disrupted protein product.
Ambry Genetics RCV001266087 SCV001444259 pathogenic Inborn genetic diseases 2019-11-26 criteria provided, single submitter clinical testing The c.3233_3236delTCAG pathogenic mutation, located in coding exon 15 of the SYNGAP1 gene, results from a deletion of 4 nucleotides at nucleotide positions 3233 to 3236, causing a translational frameshift with a predicted alternate stop codon (p.V1078Afs*51). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.
GeneDx RCV003322802 SCV004028240 pathogenic not provided 2023-02-15 criteria provided, single submitter clinical testing Reported in patients with clinical features including epilepsy and cognitive impairment in the literature (Jimenez-Gomez e al., 2019; Truty et al., 2019); 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: 26989088, 23708187, 23161826, 31440721, 31395010)

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