ClinVar Miner

Submissions for variant NM_001355436.2(SPTB):c.5266C>T (p.Arg1756Ter)

dbSNP: rs267607086
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego RCV000013696 SCV000996251 pathogenic Hereditary spherocytosis type 2 2019-02-22 criteria provided, single submitter clinical testing This nonsense variant found in exon 25 of 35 is predicted to result in loss of normal protein function. This variant has been previously reported as heterozygous change in patients with hereditary spherocytosis (PMID 19538529, 26830532). It is absent from the ExAC and gnomAD population databases and thus is presumed to be rare. Analysis of the parental samples was negative for the variant, indicating this variant likely occurred as a de novo event. Based on the available evidence, the c.5266C>T, p.Arg1756Ter variant is classified as Pathogenic.
Mayo Clinic Laboratories, Mayo Clinic RCV001508363 SCV001714475 pathogenic not provided 2020-07-21 criteria provided, single submitter clinical testing PVS1_strong, PS4, PM2, PS3
MGZ Medical Genetics Center RCV000013696 SCV002581079 pathogenic Hereditary spherocytosis type 2 2022-07-28 criteria provided, single submitter clinical testing
Invitae RCV001508363 SCV003442309 pathogenic not provided 2023-11-16 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg1756*) in the SPTB gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SPTB are known to be pathogenic (PMID: 1391962, 1498324, 8844207, 26830532, 27292444). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with hereditary spherocytosis (PMID: 19538529, 26830532, 31602632, 32436265). ClinVar contains an entry for this variant (Variation ID: 12843). For these reasons, this variant has been classified as Pathogenic.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001508363 SCV003800565 pathogenic not provided 2022-04-07 criteria provided, single submitter clinical testing The SPTB c.5266C>T; p.Arg1756 variant (rs267607086) is reported in the literature in at least 12 individuals affected with hereditary spherocytosis (Aggarwal 2020, Maciag 2009, Park 2016, Tole 2020). This variant is also reported in ClinVar (Variation ID: 12843). This variant is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. This variant induces an early termination codon and is predicted to result in a truncated protein or mRNA subject to nonsense-mediated decay. Based on available information, this variant is considered to be pathogenic.
Revvity Omics, Revvity RCV001508363 SCV003819675 pathogenic not provided 2023-04-18 criteria provided, single submitter clinical testing
OMIM RCV000013696 SCV000033943 pathogenic Hereditary spherocytosis type 2 2009-08-01 no assertion criteria provided literature only

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