ClinVar Miner

Submissions for variant NM_006772.3(SYNGAP1):c.1285C>T (p.Arg429Trp)

gnomAD frequency: 0.00002  dbSNP: rs748333558
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV000415840 SCV000493201 uncertain significance not provided 2016-08-01 criteria provided, single submitter clinical testing
Claritas Genomics RCV000449511 SCV000537842 uncertain significance Global developmental delay 2017-02-21 criteria provided, single submitter clinical testing
Invitae RCV001238256 SCV001411056 likely benign Intellectual disability, autosomal dominant 5 2023-06-23 criteria provided, single submitter clinical testing
GeneDx RCV000415840 SCV001995523 uncertain significance not provided 2023-10-24 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
New York Genome Center RCV001238256 SCV002099419 uncertain significance Intellectual disability, autosomal dominant 5 2021-02-26 criteria provided, single submitter clinical testing The de novo heterozygous missense c.1285C>T (p.Arg429Trp) variant identified in the SYNGAP1 gene of this individual has not been reported in affected individuals in the literature. It has been reported in the ClinVar database as a variant of uncertain significance (2) and likely benign (1) [Variation ID:374457]. The variant has 0.00001971 allele frequency in the gnomAD(v3) database (3 out of 152,206 heterozygous alleles, no homozygotes) suggesting it is not a common benign allele in the populations represented in that database. The affected residue is not well conserved. In silico tools provide conflicting predictions about potential pathogenicity of this variant [CADD score = 25.9, REVEL score =0.282]. Functional studies to evaluate the functional consequences of this variant have not been reported. Given the lack of compelling evidence about its pathogenicity, the de novo heterozygous missense c.1285C>T (p.Arg429Trp) variant identified in the SYNGAP1 gene is reported here as a variant of uncertain significance.

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