NM_006516.4(SLC2A1):c.1186_1188delinsTGA (p.Ser396Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 18, 2017
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000520991.1

Allele description [Variation Report for NM_006516.4(SLC2A1):c.1186_1188delinsTGA (p.Ser396Ter)]

NM_006516.4(SLC2A1):c.1186_1188delinsTGA (p.Ser396Ter)

Gene:

SLC2A1:solute carrier family 2 member 1 [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

1p34.2

Genomic location:

Preferred name:

NM_006516.4(SLC2A1):c.1186_1188delinsTGA (p.Ser396Ter)

HGVS:

NC_000001.11:g.42927695_42927697delinsTCA
NG_008232.1:g.36480_36482delinsTGA
NM_006516.4:c.1186_1188delinsTGAMANE SELECT
NP_006507.2:p.Ser396Ter
LRG_1132:g.36480_36482delinsTGA
NC_000001.10:g.43393366_43393368delinsTCA
NM_006516.2:c.1186_1188delAGCinsTGA

Protein change:

S396*

Links:

dbSNP: rs1553155885

NCBI 1000 Genomes Browser:

rs1553155885

Molecular consequence:

NM_006516.4:c.1186_1188delinsTGA - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000618384	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Aug 18, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000618384

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Aug 18, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000618384.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The c.1186_1188delAGCinsTGA pathogenic variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.1186_1188delAGCinsTGA variant results in an in-frame deletion of a single Serine residue and the insertion of a premature Stop codon at amino acid position 396, denoted S396X. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.1186_1188delAGCinsTGA variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). Therefore, the presence of c.1186_1188delAGCinsTGA is consistent with the diagnosis of Glut1-DS in this individual.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 23, 2022

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