ClinVar Miner

Submissions for variant NM_001365999.1(SZT2):c.6185G>A (p.Arg2062Gln)

gnomAD frequency: 0.00038  dbSNP: rs200443293
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV002312798 SCV000847293 uncertain significance Inborn genetic diseases 2019-02-06 criteria provided, single submitter clinical testing The p.R2005Q variant (also known as c.6014G>A), located in coding exon 42 of the SZT2 gene, results from a G to A substitution at nucleotide position 6014. The arginine at codon 2005 is replaced by glutamine, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Invitae RCV000817368 SCV000957923 uncertain significance not provided 2022-10-31 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 2005 of the SZT2 protein (p.Arg2005Gln). This variant is present in population databases (rs200443293, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with SZT2-related conditions. ClinVar contains an entry for this variant (Variation ID: 588078). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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.
GeneDx RCV000817368 SCV001772195 uncertain significance not provided 2023-08-07 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
Fulgent Genetics, Fulgent Genetics RCV002477655 SCV002788116 uncertain significance Developmental and epileptic encephalopathy, 18 2022-04-06 criteria provided, single submitter clinical testing
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV002477655 SCV003920521 uncertain significance Developmental and epileptic encephalopathy, 18 2021-11-11 criteria provided, single submitter clinical testing This variant has not been reported in the literature but is present in 0.001% (1/68022) of European alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/1-43435309-G-A?dataset=gnomad_r3). This variant is present in ClinVar (Variation ID:588078). Evolutionary conservation and computational predictive tools suggest that this variant may impact the protein. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
Genome-Nilou Lab RCV002477655 SCV004178925 uncertain significance Developmental and epileptic encephalopathy, 18 2023-04-11 criteria provided, single submitter clinical testing
New York Genome Center RCV000716452 SCV001431099 uncertain significance Seizure 2020-02-26 no assertion criteria provided clinical testing

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