NM_006516.4(SLC2A1):c.1075-16_1076del AND GLUT1 deficiency syndrome 1, autosomal recessive

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Aug 4, 2020
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:: RCV001379801.4

Allele description [Variation Report for NM_006516.4(SLC2A1):c.1075-16_1076del]

NM_006516.4(SLC2A1):c.1075-16_1076del

Gene:

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

Variant type:

Deletion

Cytogenetic location:

1p34.2

Genomic location:

Preferred name:

NM_006516.4(SLC2A1):c.1075-16_1076del

HGVS:

NC_000001.11:g.42927807_42927824del
NG_008232.1:g.36353_36370del
NM_006516.4:c.1075-16_1076delMANE SELECT
LRG_1132:g.36353_36370del
NC_000001.10:g.43393478_43393495del

Links:

dbSNP: rs2124446605

NCBI 1000 Genomes Browser:

rs2124446605

Molecular consequence:

NM_006516.4:c.1075-16_1076del - splice acceptor variant - [Sequence Ontology: SO:0001574]

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
SCV001577672	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Aug 4, 2020)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 21832227, 26193382, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001577672

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Aug 4, 2020)

germline

clinical testing

PubMed (3)
[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

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

From splitting GLUT1 deficiency syndromes to overlapping phenotypes.

Hully M, Vuillaumier-Barrot S, Le Bizec C, Boddaert N, Kaminska A, Lascelles K, de Lonlay P, Cances C, des Portes V, Roubertie A, Doummar D, LeBihannic A, Degos B, de Saint Martin A, Flori E, Pedespan JM, Goldenberg A, Vanhulle C, Bekri S, Roubergue A, Heron B, Cournelle MA, et al.

Eur J Med Genet. 2015 Sep;58(9):443-54. doi: 10.1016/j.ejmg.2015.06.007. Epub 2015 Jul 17.

PubMed [citation]

PMID:: 26193382

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001577672.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Loss-of-function variants in SLC2A1 are known to be pathogenic (PMID: 21832227, 26193382). This variant has not been reported in the literature in individuals with SLC2A1-related conditions. This variant is not present in population databases (ExAC no frequency). This variant results in the deletion of part of exon 9 (c.1075-16_1076del) of the SLC2A1 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product.

#	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: Feb 14, 2024

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