ClinVar Miner

Submissions for variant NM_001148.6(ANK2):c.7183A>C (p.Thr2395Pro) (rs201693280)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000537225 SCV000627663 uncertain significance Long QT syndrome 2020-09-09 criteria provided, single submitter clinical testing This sequence change replaces threonine with proline at codon 2395 of the ANK2 protein (p.Thr2395Pro). The threonine residue is weakly conserved and there is a small physicochemical difference between threonine and proline. This variant is present in population databases (rs201693280, ExAC 0.06%), and has an allele count higher than expected for a pathogenic variant (PMID: 28166811). This variant has been reported in an individual affected with long QT syndrome (PMID: 24981977). ClinVar contains an entry for this variant (Variation ID: 457049). 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: Possibly Damaging; 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.
Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease,Montreal Heart Institute RCV001256865 SCV001433357 uncertain significance Conduction disorder of the heart 2019-06-20 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001264520 SCV001442715 likely benign not specified 2020-10-26 criteria provided, single submitter clinical testing Variant summary: ANK2 c.7183A>C (p.Thr2395Pro) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00018 in 250596 control chromosomes, predominantly at a frequency of 0.00046 within the Latino subpopulation in the gnomAD database. The observed variant frequency within Latino control individuals in the gnomAD database is approximately 69 fold of the estimated maximal expected allele frequency for a pathogenic variant in ANK2 causing Long QT Syndrome phenotype (6.7e-06), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Latino origin. c.7183A>C has been reported in the literature in individuals affected with Long QT Syndrome, hypertrophic cardiomyopathy and adult-onset sudden cardiac death (Lopes_2013, Brion_2014, Campuzano_2017). These reports do not provide unequivocal conclusions about association of the variant with Long QT Syndrome. One co-occurrence with another pathogenic variant has been internally reported (SCN5A c.5443_5446delTCTG, p.Ser1815ThrfsX18), providing supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Three ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance (3x). Based on the evidence outlined above, the variant was classified as likely benign.
Stanford Center for Inherited Cardiovascular Disease,Stanford University RCV000786103 SCV000924747 uncertain significance not provided 2017-03-17 no assertion criteria provided provider interpretation

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