ClinVar Miner

Submissions for variant NM_005506.4(SCARB2):c.1010T>C (p.Met337Thr) (rs147324129)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Bioinformatics Core,Luxembourg Center for Systems Biomedicine RCV000655991 SCV000588267 pathogenic Rolandic epilepsy 2017-01-01 no assertion criteria provided case-control CAADphred>15
Fulgent Genetics,Fulgent Genetics RCV000765787 SCV000897176 uncertain significance Epilepsy, progressive myoclonic 4, with or without renal failure 2018-10-31 criteria provided, single submitter clinical testing
GeneDx RCV000188802 SCV000242426 uncertain significance not provided 2018-05-02 criteria provided, single submitter clinical testing The M337T variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The M337T variant is observed in 3/24034 (0.01%) alleles from individuals of African background (Lek et al., 2016). The M337T variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. In-silico analyses, including protein predictors and evolutionary conservation, support a deleterious effect. Based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Invitae RCV000555823 SCV000636456 uncertain significance Progressive myoclonic epilepsy 2018-08-02 criteria provided, single submitter clinical testing This sequence change replaces methionine with threonine at codon 337 of the SCARB2 protein (p.Met337Thr). The methionine residue is moderately conserved and there is a moderate physicochemical difference between methionine and threonine. This variant is present in population databases (rs147324129, ExAC 0.02%). This variant has been observed in an individual affected with Rolandic epilepsy (PMID: 29358611). ClinVar contains an entry for this variant (Variation ID: 206715). 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: "Benign"; Align-GVGD: "Class C0"). 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.

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