ClinVar Miner

Submissions for variant NM_001365999.1(SZT2):c.8811del (p.Ser2938fs)

dbSNP: rs745420974
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000798389 SCV000938005 pathogenic not provided 2023-10-29 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Ser2881Hisfs*41) 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). This variant is present in population databases (rs771728311, gnomAD 0.006%). 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: 644467). For these reasons, this variant has been classified as Pathogenic.
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center RCV001814237 SCV002061419 likely pathogenic Developmental and epileptic encephalopathy, 18 2021-06-27 criteria provided, single submitter clinical testing PVS1, PM2
Ambry Genetics RCV002370099 SCV002684238 pathogenic Inborn genetic diseases 2018-01-10 criteria provided, single submitter clinical testing The c.8640delC pathogenic mutation, located in coding exon 61 of the SZT2 gene, results from a deletion of one nucleotide at nucleotide position 8640, causing a translational frameshift with a predicted alternate stop codon (p.S2881Hfs*41). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.
GeneDx RCV000798389 SCV002756658 likely pathogenic not provided 2022-11-18 criteria provided, single submitter clinical testing Frameshift 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); Observed with a second SZT2 variant on the opposite allele (in trans) in a patient with infantile spasms, developmental delay, and focal seizures; however this patient also had a variant in another gene associated with epilpsy (Rochtus et al., 2020); This variant is associated with the following publications: (PMID: 31957018)
Institute of Human Genetics, University of Leipzig Medical Center RCV001814237 SCV002765125 pathogenic Developmental and epileptic encephalopathy, 18 2022-12-08 criteria provided, single submitter clinical testing This variant was identified together with NM_015284.4:c.4550G>A in the same patient._x000D_ Criteria applied: PVS1, PS4_MOD, PM2_SUP
Genome-Nilou Lab RCV001814237 SCV004178039 likely pathogenic Developmental and epileptic encephalopathy, 18 2023-04-11 criteria provided, single submitter clinical testing

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