Submissions for variant NM_172201.2(KCNE2):c.317C>T (p.Ser106Leu)

Minimum review status:		Collection method:
Minimum conflict level: Report conflict between different conditions
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Total submissions: 3

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Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000439315	SCV000515907	uncertain significance	not provided	2017-02-13	criteria provided, single submitter	clinical testing	The S106L variant of uncertain significance in the KCNE2 gene has been previously reported in one individualreferred for LQTS genetic testing, although no clinical information or segregation data was provided (Lieve et al.,2013). This variant has also been identified in other individuals referred for genetic testing at GeneDx; however, thusfar, segregation data is limited for these individuals due to the lack of clinical information provided and insufficientparticipation by informative family members. This variant is not observed at a significant frequency in largepopulation cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). In addition,S106L is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as theseresidues differ in polarity, charge, size and/or other properties. Nevertheless, S106L occurs at a position that is notconserved across species, and L106 is tolerated in at least two species. Furthermore, the majority of in silico toolspredicts this variant likely does not alter the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is pathogenic or rare benign.
Invitae	RCV001088045	SCV000549135	likely benign	Long QT syndrome 6	2023-12-06	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV000620110	SCV000737505	likely benign	Cardiovascular phenotype	2022-04-12	criteria provided, single submitter	clinical testing	This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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