ClinVar Miner

Submissions for variant NM_001365999.1(SZT2):c.5872C>T (p.Arg1958Ter)

gnomAD frequency: 0.00003  dbSNP: rs145577757
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000760923 SCV000890819 likely pathogenic not provided 2022-12-21 criteria provided, single submitter clinical testing Nonsense 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); Has not been previously published as pathogenic or benign to our knowledge
Invitae RCV000760923 SCV001216829 pathogenic not provided 2022-03-14 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg1901*) in the SZT2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SZT2 are known to be pathogenic (PMID: 23932106, 27248490, 28556953). For these reasons, this variant has been classified as Pathogenic. 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: 620537). This variant has not been reported in the literature in individuals affected with SZT2-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database.
Genetic Services Laboratory, University of Chicago RCV000760923 SCV002064326 pathogenic not provided 2018-03-07 criteria provided, single submitter clinical testing
Ambry Genetics RCV002533854 SCV003562094 pathogenic Inborn genetic diseases 2021-05-05 criteria provided, single submitter clinical testing The c.5701C>T (p.R1901*) alteration, located in exon 40 (coding exon 40) of the SZT2 gene, consists of a C to T substitution at nucleotide position 5701. This changes the amino acid from an arginine (R) to a stop codon at amino acid position 1901. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. Based on data from the Genome Aggregation Database (gnomAD) database, the SZT2 c.5701C>T alteration was observed in <0.01% (2/221402) of total alleles studied. Based on the available evidence, this alteration is classified as pathogenic.
Genome-Nilou Lab RCV003457794 SCV004177814 likely pathogenic Developmental and epileptic encephalopathy, 18 2023-04-11 criteria provided, single submitter clinical testing

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