ClinVar Miner

Submissions for variant NM_001111125.3(IQSEC2):c.2514G>T (p.Arg838=)

gnomAD frequency: 0.00003  dbSNP: rs1167090163
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001055329 SCV001219716 uncertain significance Intellectual disability, X-linked 1 2022-12-26 criteria provided, single submitter clinical testing In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 851029). This variant has not been reported in the literature in individuals affected with IQSEC2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change affects codon 838 of the IQSEC2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the IQSEC2 protein.
GeneDx RCV002307668 SCV002601223 uncertain significance not provided 2022-11-10 criteria provided, single submitter clinical testing In silico analysis supports a deleterious effect on splicing; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge
Clinical Genomics Laboratory, Washington University in St. Louis RCV001055329 SCV004176959 uncertain significance Intellectual disability, X-linked 1 2023-08-27 criteria provided, single submitter clinical testing The IQSEC2 c.2514G>T (p.Arg838=) variant has not been reported in the medical literature to our knowledge. This variant is absent from the general population (gnomAD v.2.1.1), indicating it is not a common variant. Computational predictors indicate that this variant would alter RNA splicing, evidence that correlates with impact to IQSEC2 protein function. This variant has been submitted to ClinVar as a variant of uncertain significance by two laboratories (variation ID: 851029). Due to limited information, and based on ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), the clinical significance of this variant is uncertain at this time.

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