ClinVar Miner

Submissions for variant NM_006279.5(ST3GAL3):c.781C>T (p.Arg261Ter)

gnomAD frequency: 0.00001  dbSNP: rs1195818093
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001994497 SCV002234173 pathogenic Early infantile epileptic encephalopathy with suppression bursts 2022-06-24 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with ST3GAL3-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.003%). This sequence change creates a premature translational stop signal (p.Arg261*) in the ST3GAL3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ST3GAL3 are known to be pathogenic (PMID: 31584066).
Ambry Genetics RCV002407174 SCV002670810 pathogenic Inborn genetic diseases 2018-03-09 criteria provided, single submitter clinical testing The p.R261* pathogenic mutation (also known as c.781C>T), located in coding exon 9 of the ST3GAL3 gene, results from a C to T substitution at nucleotide position 781. This changes the amino acid from an arginine to a stop codon within coding exon 9. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV003224596 SCV003920509 pathogenic Intellectual disability, autosomal recessive 12; Developmental and epileptic encephalopathy, 15 2022-12-05 criteria provided, single submitter clinical testing This variant has not been reported in the literature but is present in the Genome Aggregation Database (Highest reported MAF 0.001% (1/68000) (https://gnomad.broadinstitute.org/variant/1-43920440-C-T?dataset=gnomad_r3). This variant is present in ClinVar (Variation ID:1452219). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. This variant creates a premature stop at this codon which results in an absent or abnormal protein. Loss of function variants have been reported in association with disease for this gene (Indellicato 2020 PMID:31584066). In summary, data on this variant is highly suspicious for disease, but requires further evidence for pathogenicity. Therefore, this variant is classified as likely pathogenic.

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