NM_006516.4(SLC2A1):c.835C>T (p.Gln279Ter) AND GLUT1 deficiency syndrome 1, autosomal recessive

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 13, 2022
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:: RCV000559813.7

Allele description [Variation Report for NM_006516.4(SLC2A1):c.835C>T (p.Gln279Ter)]

NM_006516.4(SLC2A1):c.835C>T (p.Gln279Ter)

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.835C>T (p.Gln279Ter)

HGVS:

NC_000001.11:g.42929625G>A
NG_008232.1:g.34552C>T
NM_006516.4:c.835C>TMANE SELECT
NP_006507.2:p.Gln279Ter
LRG_1132:g.34552C>T
NC_000001.10:g.43395296G>A
NM_006516.2:c.835C>T

Protein change:

Q279*

Links:

dbSNP: rs1553156051

NCBI 1000 Genomes Browser:

rs1553156051

Molecular consequence:

NM_006516.4:c.835C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV000649811	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 13, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 25487684, 21832227, 26193382, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000649811

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 13, 2022)

germline

clinical testing

PubMed (4)
[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

Nationwide survey of glucose transporter-1 deficiency syndrome (GLUT-1DS) in Japan.

Ito Y, Takahashi S, Kagitani-Shimono K, Natsume J, Yanagihara K, Fujii T, Oguni H.

Brain Dev. 2015 Sep;37(8):780-9. doi: 10.1016/j.braindev.2014.11.006. Epub 2014 Dec 5.

PubMed [citation]

PMID:: 25487684

Paroxysmal choreoathetosis/spasticity (DYT9) is caused by a GLUT1 defect.

Weber YG, Kamm C, Suls A, Kempfle J, Kotschet K, Schüle R, Wuttke TV, Maljevic S, Liebrich J, Gasser T, Ludolph AC, Van Paesschen W, Schöls L, De Jonghe P, Auburger G, Lerche H.

Neurology. 2011 Sep 6;77(10):959-64. doi: 10.1212/WNL.0b013e31822e0479. Epub 2011 Aug 10.

PubMed [citation]

PMID:: 21832227

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000649811.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 471349). This premature translational stop signal has been observed in individual(s) with glucose transporter-1 deficiency syndrome (PMID: 25487684, 26193382). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln279*) in the SLC2A1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC2A1 are known to be pathogenic (PMID: 21832227, 26193382).

#	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: Sep 29, 2024

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