NM_006516.4(SLC2A1):c.1250T>C (p.Ile417Thr) AND GLUT1 deficiency syndrome 1, autosomal recessive

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 30, 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:: RCV000812546.8

Allele description

NM_006516.4(SLC2A1):c.1250T>C (p.Ile417Thr)

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.1250T>C (p.Ile417Thr)

HGVS:

NC_000001.11:g.42927633A>G
NG_008232.1:g.36544T>C
NM_006516.4:c.1250T>CMANE SELECT
NP_006507.2:p.Ile417Thr
LRG_1132:g.36544T>C
NC_000001.10:g.43393304A>G
NM_006516.2:c.1250T>C

Protein change:

I417T

Links:

dbSNP: rs144389023

NCBI 1000 Genomes Browser:

rs144389023

Molecular consequence:

NM_006516.4:c.1250T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

Recent activity

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Homo sapiens zinc finger and SCAN domain containing 1 (ZSCAN1), mRNA
Homo sapiens zinc finger and SCAN domain containing 1 (ZSCAN1), mRNA
gi|110431335|ref|NM_182572.3|

Nucleotide
PREDICTED: Homo sapiens ATP binding cassette subfamily C member 9 (ABCC9), trans...
PREDICTED: Homo sapiens ATP binding cassette subfamily C member 9 (ABCC9), transcript variant X1, mRNA
gi|2462529191|ref|XM_054370717.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000952864	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 30, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 26193382, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000952864

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 30, 2023)

germline

clinical testing

PubMed (2)
[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

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000952864.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant is present in population databases (rs144389023, gnomAD 0.07%). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (Invitae) did not meet the statistical confidence thresholds required to predict the impact of this variant on SLC2A1 function. ClinVar contains an entry for this variant (Variation ID: 656192). This missense change has been observed in individual(s) with glucose transporter type 1 deficiency syndrome (GLUT1DS) (PMID: 26193382). This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 417 of the SLC2A1 protein (p.Ile417Thr).

#	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 20, 2024

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