NM_006516.4(SLC2A1):c.940G>A (p.Gly314Ser) AND GLUT1 deficiency syndrome 1, autosomal recessive

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 14, 2024
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:: RCV000473987.19

Allele description [Variation Report for NM_006516.4(SLC2A1):c.940G>A (p.Gly314Ser)]

NM_006516.4(SLC2A1):c.940G>A (p.Gly314Ser)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

1p34.2

Genomic location:

Preferred name:

NM_006516.4(SLC2A1):c.940G>A (p.Gly314Ser)

HGVS:

NC_000001.11:g.42929242C>T
NG_008232.1:g.34935G>A
NM_006516.4:c.940G>AMANE SELECT
NP_006507.2:p.Gly314Ser
NP_006507.2:p.Gly314Ser
LRG_1132:g.34935G>A
NC_000001.10:g.43394913C>T
NM_006516.2:c.940G>A
P11166:p.Gly314Ser

Protein change:

G314S; GLY314SER

Links:

UniProtKB: P11166#VAR_054764; OMIM: 138140.0009; dbSNP: rs121909739

NCBI 1000 Genomes Browser:

rs121909739

Molecular consequence:

NM_006516.4:c.940G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: GLUT1 deficiency syndrome 1, autosomal recessive
Identifiers:: MedGen: C3149117

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000545828	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 14, 2024)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 11076005, 26615598, 27351150, 18451999, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000545828

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 14, 2024)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Familial paroxysmal exercise-induced dyskinesia and benign epilepsy: a clinical and neurophysiological study of an uncommon disorder.

Margari L, Perniola T, Illiceto G, Ferrannini E, De Iaco MG, Presicci A, Santostasi R, Ventura P.

Neurol Sci. 2000 Jun;21(3):165-72.

PubMed [citation]

PMID:: 11076005

CoQ(10) Deficiency Is Not a Common Finding in GLUT1 Deficiency Syndrome.

Barca E, Tang M, Kleiner G, Engelstad K, DiMauro S, Quinzii CM, De Vivo DC.

JIMD Rep. 2016;29:47-52. Epub 2015 Nov 29.

PubMed [citation]

PMID:: 26615598
PMCID:: PMC5059199

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000545828.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 314 of the SLC2A1 protein (p.Gly314Ser). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with epilepsy, mild mental retardation, and impulsivity and/or paroxysmal exertion-induced dyskinesias (PMID: 11076005, 18451999, 26615598, 27351150). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 16113). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt SLC2A1 protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects SLC2A1 function (PMID: 18451999). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Nov 3, 2024

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