Submissions for variant NM_001130438.3(SPTAN1):c.6019_6020del (p.Thr2006_Asp2007insTer)

Total submissions: 2

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Labcorp Genetics (formerly Invitae), Labcorp	RCV002861659	SCV003219286	pathogenic	Early infantile epileptic encephalopathy with suppression bursts	2023-01-10	criteria provided, single submitter	clinical testing	For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with SPTAN1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Asp2007*) in the SPTAN1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SPTAN1 are known to be pathogenic (PMID: 31332438, 33206935).
PreventionGenetics, part of Exact Sciences	RCV004548372	SCV004109656	likely pathogenic	SPTAN1-related disorder	2023-06-07	criteria provided, single submitter	clinical testing	The SPTAN1 c.6019_6020delGA variant is predicted to result in premature protein termination (p.Asp2007*). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Premature protein truncating variants in SPTAN1 are expected to be pathogenic. This variant is interpreted as likely pathogenic.