Total submissions: 5
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Gene |
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, |
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- |
RCV003457794 | SCV004177814 | likely pathogenic | Developmental and epileptic encephalopathy, 18 | 2023-04-11 | criteria provided, single submitter | clinical testing |