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NM_006516.4(SLC2A1):c.312C>G (p.Phe104Leu)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Sep 28, 2021)
Last evaluated:
Aug 29, 2020
Accession:
VCV000297381.6
Variation ID:
297381
Description:
single nucleotide variant
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NM_006516.4(SLC2A1):c.312C>G (p.Phe104Leu)

Allele ID
280596
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p34.2
Genomic location
1: 42930830 (GRCh38) GRCh38 UCSC
1: 43396501 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.11:g.42930830G>C
NG_008232.1:g.33347C>G
NM_006516.4:c.312C>G MANE Select NP_006507.2:p.Phe104Leu missense
... more HGVS
Protein change
F104L
Other names
-
Canonical SPDI
NC_000001.11:42930829:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00010
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00023
Trans-Omics for Precision Medicine (TOPMed) 0.00008
Links
ClinGen: CA803560
dbSNP: rs76672402
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000311944.2
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000350448.2
Likely benign 1 criteria provided, single submitter Nov 21, 2016 RCV000480070.2
Benign 1 criteria provided, single submitter Aug 29, 2020 RCV000864633.3
Likely benign 1 criteria provided, single submitter Jan 28, 2020 RCV001711886.1
not provided 1 no assertion provided - RCV000662334.1

Clinical features observed in individuals with this variant

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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SLC2A1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
642 666

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
GLUT1 deficiency syndrome 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000357707.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Dystonia 9
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000357708.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Likely benign
(Nov 21, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000703136.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Aug 29, 2020)
criteria provided, single submitter
Method: clinical testing
GLUT1 deficiency syndrome 1, autosomal recessive
Allele origin: germline
Invitae
Accession: SCV001005460.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jan 28, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000565576.4
Submitted: (Sep 28, 2021)
Evidence details
not provided
(-)
no assertion provided
Method: phenotyping only
GLUT1 deficiency syndrome 2
Allele origin: unknown
GenomeConnect, ClinGen
Accession: SCV000784692.1
Submitted: (Mar 13, 2018)
Evidence details
Comment:
GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SLC2A1 - - - -

Text-mined citations for rs76672402...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 30, 2021