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NM_006516.4(SLC2A1):c.680-3C>G AND Encephalopathy due to GLUT1 deficiency

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Oct 2, 2021
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:
RCV001775326.1

Allele description [Variation Report for NM_006516.4(SLC2A1):c.680-3C>G]

NM_006516.4(SLC2A1):c.680-3C>G

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.680-3C>G
HGVS:
  • NC_000001.11:g.42929783G>C
  • NG_008232.1:g.34394C>G
  • NM_006516.4:c.680-3C>GMANE SELECT
  • LRG_1132:g.34394C>G
  • NC_000001.10:g.43395454G>C
  • NM_006516.2:c.680-3C>G
Links:
dbSNP: rs112081052
NCBI 1000 Genomes Browser:
rs112081052
Molecular consequence:
  • NM_006516.4:c.680-3C>G - intron variant - [Sequence Ontology: SO:0001627]
Observations:
1

Condition(s)

Name:
Encephalopathy due to GLUT1 deficiency
Synonyms:
De Vivo disease; Glucose transport defect, blood-brain barrier; Glucose transporter protein syndrome; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0011724; MedGen: C4551966; Orphanet: 71277; OMIM: 606777

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV0020121213billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Oct 2, 2021) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot provided1not providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From 3billion, SCV002012121.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The variant was observed as assumed (i.e. paternity and maternity not confirmed) de novoo (3billion dataset, PM6). It is not observed in the gnomAD v2.1.1 dataset (PM2).In silico tools predict the variant to alter splicing and produce an abnormal transcript (ADA:0.99, RF 0.954, PP3 ). Patient's phenotype is considered compatible with GLUT1 deficiency syndrome 1, infantile onset, severe (3billion dataset, PP4). Therefore, this variant is classified as likely pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Dec 24, 2023