Submissions for variant NM_144643.4(SCLT1):c.1843C>T (p.Arg615Ter)

Total submissions: 2

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Labcorp Genetics (formerly Invitae), Labcorp	RCV005059875	SCV005698834	pathogenic	not provided	2024-10-05	criteria provided, single submitter	clinical testing	This sequence change creates a premature translational stop signal (p.Arg615*) in the SCLT1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SCLT1 are known to be pathogenic (PMID: 28005958). This variant is present in population databases (rs115634955, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with SCLT1-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
PreventionGenetics, part of Exact Sciences	RCV004737626	SCV005357705	uncertain significance	SCLT1-related disorder	2024-07-24	no assertion criteria provided	clinical testing	The SCLT1 c.1843C>T variant is predicted to result in premature protein termination (p.Arg615*). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0029% of alleles in individuals of Latino descent in gnomAD. Although we suspect that this variant may be pathogenic, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.