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NM_006516.4(SLC2A1):c.1395C>T (p.Ser465=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(2);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Sep 30, 2021)
Last evaluated:
Apr 22, 2021
Accession:
VCV000212203.7
Variation ID:
212203
Description:
single nucleotide variant
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NM_006516.4(SLC2A1):c.1395C>T (p.Ser465=)

Allele ID
206798
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p34.2
Genomic location
1: 42927125 (GRCh38) GRCh38 UCSC
1: 43392796 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.11:g.42927125G>A
NG_008232.1:g.37052C>T
NM_006516.4:c.1395C>T MANE Select NP_006507.2:p.Ser465= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000001.11:42927124:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00005
The Genome Aggregation Database (gnomAD) 0.00008
Exome Aggregation Consortium (ExAC) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00004
The Genome Aggregation Database (gnomAD) 0.00010
Trans-Omics for Precision Medicine (TOPMed) 0.00003
Links
ClinGen: CA207542
dbSNP: rs75852730
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Feb 12, 2015 RCV000193808.5
Likely benign 1 criteria provided, single submitter Oct 9, 2020 RCV000648092.4
Uncertain significance 1 criteria provided, single submitter Dec 5, 2017 RCV000768318.1
Likely benign 1 criteria provided, single submitter Apr 22, 2021 RCV001721262.1
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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
647 671

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Feb 12, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000248912.1
Submitted: (Sep 15, 2015)
Evidence details
Uncertain significance
(Dec 05, 2017)
criteria provided, single submitter
Method: clinical testing
Dystonia 9
GLUT1 deficiency syndrome 1
GLUT1 deficiency syndrome 2
Stomatin-deficient cryohydrocytosis with neurologic defects
Epilepsy, idiopathic generalized, susceptibility to, 12
Allele origin: germline
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
Accession: SCV000898978.1
Submitted: (Dec 12, 2018)
Evidence details
Comment:
SLC2A1 NM_006516.2 exon 10 p.Ser465= (c.1395C>T): This variant has not been reported in the literature but is present in 4/34420 Latino alleles in the Genome … (more)
Likely benign
(Oct 09, 2020)
criteria provided, single submitter
Method: clinical testing
GLUT1 deficiency syndrome 1, autosomal recessive
Allele origin: germline
Invitae
Accession: SCV000769902.4
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Apr 22, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000514687.5
Submitted: (Sep 30, 2021)
Evidence details

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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs75852730...

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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 Nov 27, 2021