Submissions for variant NM_006516.4(SLC2A1):c.2T>C (p.Met1Thr)

dbSNP: rs1553157935

Total submissions: 5

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000578988	SCV000680660	pathogenic	not provided	2020-01-10	criteria provided, single submitter	clinical testing	Reported as p.Met1Thr in 16 year old female with sporadic glucose transporter type 1 deficiency syndrome (Hully et al., 2015); Not observed in large population cohorts (Lek et al., 2016); Initiation codon variant in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 26193382)
Labcorp Genetics (formerly Invitae), Labcorp	RCV002529042	SCV003523195	pathogenic	GLUT1 deficiency syndrome 1, autosomal recessive	2022-08-24	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: 488790). Disruption of the initiator codon has been observed in individual(s) with autosomal dominant Glut1 deficiency syndrome (PMID: 20129935, 26193382). This variant is not present in population databases (gnomAD no frequency). This sequence change affects the initiator methionine of the SLC2A1 mRNA. The next in-frame methionine is located at codon 13.
PreventionGenetics, part of Exact Sciences	RCV004553293	SCV004117844	likely pathogenic	SLC2A1-related disorder	2022-12-08	criteria provided, single submitter	clinical testing	The SLC2A1 c.2T>C variant is predicted to disrupt the translation initiation site (Start loss). This variant was reported in an individual with Glucose transporter type 1 deficiency syndrome (Hully et al 2015. PubMed ID: 26193382). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as likely pathogenic.
Genome-Nilou Lab	RCV003446156	SCV004174008	likely pathogenic	Encephalopathy due to GLUT1 deficiency	2023-04-11	criteria provided, single submitter	clinical testing
GenomeConnect, ClinGen	RCV001249305	SCV001423266	not provided	GLUT1 deficiency syndrome		no assertion provided	phenotyping only	Variant interpretted as Pathogenic and reported on 05-08-2019 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.