ClinVar Miner

Submissions for variant NM_001365999.1(SZT2):c.2929+1G>A

gnomAD frequency: 0.00001  dbSNP: rs1295389410
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV002541813 SCV003523196 pathogenic not provided 2021-12-24 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Studies have shown that disruption of this splice site results in skipping of exon 20 and introduces a premature termination codon (PMID: 28556953). The resulting mRNA is expected to undergo nonsense-mediated decay. ClinVar contains an entry for this variant (Variation ID: 997439). Disruption of this splice site has been observed in individual(s) with early-onset epileptic encephalopathy (PMID: 28556953). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 20 of the SZT2 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product.
OMIM RCV001292587 SCV001481160 pathogenic Developmental and epileptic encephalopathy, 18 2021-02-19 no assertion criteria provided literature only

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