NM_006516.4(SLC2A1):c.884C>T (p.Thr295Met) AND not provided

Germline classification:: Pathogenic (4 submissions)
Last evaluated:: Mar 14, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000189397.11

Allele description [Variation Report for NM_006516.4(SLC2A1):c.884C>T (p.Thr295Met)]

NM_006516.4(SLC2A1):c.884C>T (p.Thr295Met)

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.884C>T (p.Thr295Met)

Other names:

p.T295M:ACG>ATG

HGVS:

NC_000001.11:g.42929298G>A
NG_008232.1:g.34879C>T
NM_006516.4:c.884C>TMANE SELECT
NP_006507.2:p.Thr295Met
LRG_1132t1:c.884C>T
LRG_1132:g.34879C>T
NC_000001.10:g.43394969G>A
NM_006516.2:c.884C>T
NM_006516.3:c.884C>T
P11166:p.Thr295Met

Protein change:

T295M

Links:

UniProtKB: P11166#VAR_054763; dbSNP: rs80359823

NCBI 1000 Genomes Browser:

rs80359823

Molecular consequence:

NM_006516.4:c.884C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000243035	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Nov 20, 2019)	germline	clinical testing	Citation Link,
SCV001809757	Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV001958667	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV004225824	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 14, 2023)	germline	clinical testing	PubMed (11) [See all records that cite these PMIDs] 15622525, 16949238, 17052934, 18614966, 20129935, 20630673, 23740044, 29930392, 33015236, 36362347, 25741868

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Glut-1 deficiency syndrome: clinical, genetic, and therapeutic aspects.

Wang D, Pascual JM, Yang H, Engelstad K, Jhung S, Sun RP, De Vivo DC.

Ann Neurol. 2005 Jan;57(1):111-8.

PubMed [citation]

PMID:: 15622525

Three Japanese patients with glucose transporter type 1 deficiency syndrome.

Fujii T, Ho YY, Wang D, De Vivo DC, Miyajima T, Wong HY, Tsang PT, Shirasaka Y, Kudo T, Ito M.

Brain Dev. 2007 Mar;29(2):92-7. Epub 2006 Sep 1.

PubMed [citation]

PMID:: 16949238

See all PubMed Citations (11)

Details of each submission

From GeneDx, SCV000243035.16

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Published functional studies demonstrate a damaging effect on glucose transport activity (Wong HY, 2007; Wang et al., 2008; Deng et al., 2014); Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 21546317, 20630673, 22011817, 20830593, 23740044, 17052934, 18614966, 24847886, 21649651, 19798636, 16949238, 21382692, 23280796, 25487684, 17718830, 22190371, 25982116, 20186957, 29303961, 28556183, 29655203, 15622525, 32591173)

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

From Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus, SCV001809757.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

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

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001958667.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

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

From Mayo Clinic Laboratories, Mayo Clinic, SCV004225824.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (11)

Description

PP1, PP3, PP4, PM1, PM2, PM5, PM6, PS3, PS4

#	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		1	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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