ClinVar Miner

Submissions for variant NM_006363.6(SEC23B):c.890C>T (p.Thr297Ile)

gnomAD frequency: 0.00001  dbSNP: rs1363436677
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000821067 SCV000961808 uncertain significance Congenital dyserythropoietic anemia, type II; Cowden syndrome 7 2021-08-27 criteria provided, single submitter clinical testing This sequence change replaces threonine with isoleucine at codon 297 of the SEC23B protein (p.Thr297Ile). The threonine residue is highly conserved and there is a moderate physicochemical difference between threonine and isoleucine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with SEC23B-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Revvity Omics, Revvity RCV003141852 SCV003819271 uncertain significance not provided 2022-09-13 criteria provided, single submitter clinical testing
GeneDx RCV003141852 SCV004040398 uncertain significance not provided 2023-03-30 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004702456 SCV005205055 uncertain significance not specified 2024-06-07 criteria provided, single submitter clinical testing Variant summary: SEC23B c.890C>T (p.Thr297Ile) results in a non-conservative amino acid change located in the Sec23/Sec24, trunk domain (IPR006896) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251434 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.890C>T in individuals affected with SEC23B-Related Disorders and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 663227). Based on the evidence outlined above, the variant was classified as uncertain significance.

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