ClinVar Miner

Submissions for variant NM_006516.4(SLC2A1):c.988C>T (p.Arg330Ter)

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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000189360 SCV000242997 pathogenic not provided 2021-12-01 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 10980529, 25525159, 26216499, 26193382, 20129935, 29655203, 32371413, 34676189, 32712428)
Labcorp Genetics (formerly Invitae), Labcorp RCV000461498 SCV000545826 pathogenic GLUT1 deficiency syndrome 1, autosomal recessive 2022-07-25 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. ClinVar contains an entry for this variant (Variation ID: 207196). This premature translational stop signal has been observed in individual(s) with Glut-1 Deficiency Syndrome (PMID: 10980529, 20129935, 26216499). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Arg330*) in the SLC2A1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC2A1 are known to be pathogenic (PMID: 21832227, 26193382).
Ambry Genetics RCV000622452 SCV000741549 pathogenic Inborn genetic diseases 2016-06-29 criteria provided, single submitter clinical testing
Baylor Genetics RCV000679880 SCV000807266 pathogenic Encephalopathy due to GLUT1 deficiency 2017-09-01 criteria provided, single submitter clinical testing This variant has been previously reported as disease-causing and was found once in our laboratory in a 13-year-old female with intellectual disability with regression, microcephaly, cryptogenic generalized epilepsy, static encephalopathy
Génétique des Maladies du Développement, Hospices Civils de Lyon RCV001004692 SCV001164153 pathogenic Childhood onset GLUT1 deficiency syndrome 2 2017-07-11 criteria provided, single submitter clinical testing
Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital RCV001249688 SCV001423684 pathogenic Hereditary cryohydrocytosis with reduced stomatin; Dystonia 9; Encephalopathy due to GLUT1 deficiency; Childhood onset GLUT1 deficiency syndrome 2 2017-12-15 criteria provided, single submitter clinical testing [ACMG/AMP: PVS1, PS2, PM2, PP3, PP5] This alteration is a null variant in a gene where LOF is a known mechanism of disease [PVS1], is de novo in origin as it was not detected in the submitted parental specimens (identity confirmed) [PS2], is absent from or rarely observed in large-scale population databases [PM2], is predicted to be damaging by multiple functional prediction tools [PP3], was reported as a pathogenic/likely pathogenic alteration by a reputable source (ClinVar or other correspondence from a clinical testing laboratory) [PP5].
CeGaT Center for Human Genetics Tuebingen RCV000189360 SCV001500364 pathogenic not provided 2020-10-01 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000189360 SCV002020696 pathogenic not provided 2019-09-04 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000679880 SCV004172800 pathogenic Encephalopathy due to GLUT1 deficiency 2023-04-11 criteria provided, single submitter clinical testing
Laboratory of Molecular Genetics, CHU RENNES RCV000415466 SCV000493100 likely pathogenic Epilepsy; Microcephaly; intellectual deficiency no assertion criteria provided clinical testing
GenomeConnect - Brain Gene Registry RCV000679880 SCV003804779 not provided Encephalopathy due to GLUT1 deficiency no assertion provided phenotyping only Variant interpreted as Pathogenic and reported on 07-25-2022 by Invitae . Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Philip Payne PhD, FACMI from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/.

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