Submissions for variant NM_001365999.1(SZT2):c.9874C>T (p.Arg3292Ter)

gnomAD frequency: 0.00001  dbSNP: rs1302034044

Total submissions: 3

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Invitae	RCV001045979	SCV001209858	pathogenic	not provided	2022-03-19	criteria provided, single submitter	clinical testing	For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 843369). This premature translational stop signal has been observed in individual(s) with early infantile epileptic encephalopathy (PMID: 27248490). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. 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. This sequence change creates a premature translational stop signal (p.Arg3235*) 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).
Genetics Laboratory, UDIAT-Centre Diagnòstic, Hospital Universitari Parc Tauli	RCV001420267	SCV001622687	pathogenic	See cases	2021-04-26	criteria provided, single submitter	clinical testing	PVS1_very strong;PM2_supporting;PM3_supporting;PP5_supporting
Genome-Nilou Lab	RCV003457923	SCV004178103	pathogenic	Developmental and epileptic encephalopathy, 18	2023-04-11	criteria provided, single submitter	clinical testing