ClinVar Miner

Submissions for variant NM_021912.5(GABRB3):c.31C>T (p.Pro11Ser)

gnomAD frequency: 0.00354  dbSNP: rs25409
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Total submissions: 14
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia RCV000203153 SCV000258180 likely benign not specified 2015-05-11 criteria provided, single submitter clinical testing
GeneDx RCV001701568 SCV000513096 benign not provided 2019-04-08 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 26645412, 22206818, 20550555, 19935738, 18514161, 20308251, 27884173, 31435640)
Athena Diagnostics RCV000203153 SCV000613366 benign not specified 2016-12-02 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000017575 SCV000782445 uncertain significance Epilepsy, childhood absence, susceptibility to, 5 2016-05-02 criteria provided, single submitter clinical testing
Ambry Genetics RCV002313713 SCV000849397 benign Inborn genetic diseases 2016-09-16 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Mendelics RCV000989276 SCV001139532 benign Epilepsy, childhood absence, susceptibility to, 1 2019-05-28 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001511952 SCV001719277 benign Epilepsy, childhood absence, susceptibility to, 1; Epilepsy, childhood absence, susceptibility to, 5 2023-12-11 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV001701568 SCV002497748 benign not provided 2024-08-01 criteria provided, single submitter clinical testing GABRB3: PP2, BP4, BS1, BS2
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV003224101 SCV003919997 likely benign Epilepsy, childhood absence, susceptibility to, 5; Developmental and epileptic encephalopathy, 43 2022-10-24 criteria provided, single submitter clinical testing GABRB3 NM_021912.5 exon 1 p.Pro11Ser (c.31C>T): This variant has been reported in the literature in at least 2 individuals with absence epilepsy and numerous individuals with autism (Tanaka 2008 PMID:185141461, Delahanty 2011 PMID:19935738). However, this variant is present in 0.5% (370/67998) of European alleles including 2 homozygotes, as well as 1 homozygote in the South Asian population in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/15-26773694-G-A?dataset=gnomad_r3). This variant is present in ClinVar, with several labs classifying this variant as Likely Benign or Benign (Variation ID:16191). Evolutionary conservation for this variant is limited or unavailable; computational predictive tools suggest that this variant may not impact the protein. In vitro functional studies suggests that this variant may impact the protein, however, this data may not represent in vivo biological function (Tanaka 2008 PMID:185141461, Shi 2019 PMID:31435640). In summary, data on this variant, particularly the minor allele frequency and presence of homozygotes in ostensibly unaffected individuals suggests that this variant does not cause disease, but requires further evidence. Therefore this variant is classified as Likely Benign.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001701568 SCV004564680 benign not provided 2023-10-13 criteria provided, single submitter clinical testing
OMIM RCV000017575 SCV000037847 risk factor Epilepsy, childhood absence, susceptibility to, 5 2008-06-01 no assertion criteria provided literature only
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV001701568 SCV001932694 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV001701568 SCV001966306 likely benign not provided no assertion criteria provided clinical testing
PreventionGenetics, part of Exact Sciences RCV003934836 SCV004752053 benign GABRB3-related disorder 2020-06-05 no assertion criteria provided clinical testing This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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