ClinVar Miner

Submissions for variant NM_001355436.2(SPTB):c.6119C>T (p.Thr2040Ile)

dbSNP: rs1345709572
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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute RCV001089997 SCV001245014 likely pathogenic Hereditary spherocytosis type 2 2018-10-01 criteria provided, single submitter clinical testing A homozygous missense variant, NM_001024858.3(SPTB):c.6119C>T, has been identified in exon 29 of 35 of the SPTB gene. The variant is predicted to result in a moderate amino acid change from threonine to isoleucine at position 2040 of the protein, NP_001020029.1(SPTB):p.(Thr2040Ile). The threonine residue at this position has moderate conservation (100 vertebrates, UCSC), and is located within the Spectrin repeat region where all other pathogenic missense variants have been reported. In silico predictions for this variant are consistently pathogenic (Polyphen, SIFT, CADD, Mutation Taster), the variant is absent in population databases (gnomAD, dbSNP, 1000G) and has not been previously reported in clinical cases. However, eosin-5-maleimide studies are supportive of a spectrin defect. Analysis of parental samples indicated that the parents are both carriers. Based on the information available at the time of curation, this variant has been classified as LIKELY PATHOGENIC. NB: This variant has been reclassified as LIKELY PATHOGENIC due to subsequent functional analysis.

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