ClinVar Miner

Submissions for variant NM_172057.2(KCNH2):c.1676C>G (p.Thr559Arg) (rs1480554629)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000532747 SCV000627468 uncertain significance Long QT syndrome 2017-03-07 criteria provided, single submitter clinical testing This sequence change replaces threonine with arginine at codon 899 of the KCNH2 protein (p.Thr899Arg). The threonine residue is weakly conserved and there is a moderate physicochemical difference between threonine and arginine. While this variant is not present in population databases (no rs ID), the frequency information is unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has not been reported in the literature in individuals with a KCNH2-related disease. This variant identified in the KCNH2 gene is located in the cytoplasmic C-terminal region of the resulting protein (PMID: 19841300, 25348405). For more information about the location of this variant, please visit www.invitae.com/KCNH2-topology. It is unclear how this variant impacts the function of this protein. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may alter RNA splicing, but this prediction has not been confirmed by published transcriptional studies. In summary, this variant is a novel missense change with uncertain impact on protein function. It has been classified as a Variant of Uncertain Significance.
Ambry Genetics RCV000620755 SCV000737969 uncertain significance Cardiovascular phenotype 2017-03-27 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Insufficient evidence

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