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NM_006516.4(SLC2A1):c.457C>T (p.Arg153Cys) AND GLUT1 deficiency syndrome 1, autosomal recessive

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 11, 2023
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:
RCV001390268.7

Allele description [Variation Report for NM_006516.4(SLC2A1):c.457C>T (p.Arg153Cys)]

NM_006516.4(SLC2A1):c.457C>T (p.Arg153Cys)

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.457C>T (p.Arg153Cys)
HGVS:
  • NC_000001.11:g.42930685G>A
  • NG_008232.1:g.33492C>T
  • NM_006516.4:c.457C>TMANE SELECT
  • NP_006507.2:p.Arg153Cys
  • LRG_1132:g.33492C>T
  • NC_000001.10:g.43396356G>A
Protein change:
R153C
Links:
dbSNP: rs1643479461
NCBI 1000 Genomes Browser:
rs1643479461
Molecular consequence:
  • NM_006516.4:c.457C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001591945Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Aug 11, 2023) 		germlineclinical testing

PubMed (11)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Imaging the metabolic footprint of Glut1 deficiency on the brain.

Pascual JM, Van Heertum RL, Wang D, Engelstad K, De Vivo DC.

Ann Neurol. 2002 Oct;52(4):458-64.

PubMed [citation]
PMID:
12325075

Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study.

Rauch A, Wieczorek D, Graf E, Wieland T, Endele S, Schwarzmayr T, Albrecht B, Bartholdi D, Beygo J, Di Donato N, Dufke A, Cremer K, Hempel M, Horn D, Hoyer J, Joset P, Röpke A, Moog U, Riess A, Thiel CT, Tzschach A, Wiesener A, et al.

Lancet. 2012 Nov 10;380(9854):1674-82. doi: 10.1016/S0140-6736(12)61480-9. Epub 2012 Sep 27.

PubMed [citation]
PMID:
23020937
See all PubMed Citations (11)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001591945.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (11)

Description

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 153 of the SLC2A1 protein (p.Arg153Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with GLUT1-deficiency syndrome (PMID: 12325075, 23020937, 23106342, 25564316, 28556183, 29655203, 31487502). ClinVar contains an entry for this variant (Variation ID: 1076377). 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. This variant disrupts the p.Arg153 amino acid residue in SLC2A1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 20129935, 26193382, 26267703). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024