- Email: [email protected]
How Much Is Enough? Weighing the Evidence for Mutation Pathogenicity
Canadian Journal of Cardiology 28 (2012) 119.e9 –119.e10 www.onlinecjc.ca
Letters to the Editor Stacey Hume, PhD, FCCMG
How Much Is Enough? Weighing the Evidence for Mutation Pathogenicity To the Editor: We read with great interest the recent publication by Kazemian et al. in the November/December 2011 issue. The authors report a novel missense mutation in the RYR2 gene: S4153R or A12457C (recommended Human Genome Variation Society nomenclature: p.Ser4153Arg, c.12457A⬎C). This sequence variant is in a residue conserved among mammals, in a domain II “hotspot” region of the RYR2 gene, and results in a nonsynonymous amino acid change. Therefore, one might suspect it to be disease causing, ie, a pathogenic mutation. Recommendations for the interpretation and reporting of sequence variations have been published.1 Several factors that may suggest that a variant is a deleterious mutation include cosegregation of the variant with the disease in the family, increased prevalence of the variant in cases vs healthy controls, sequence conservation between species, the nature of the amino acid substitution, and protein functional analysis.1 In this case, CASQ2 screening, family cosegregation studies, and functional analysis were not performed. Additionally, the prevalence of this variant in healthy controls has not been studied. Recently others have reported on the inherent difficulties in interpreting novel sequence variants.2-4 Variants have been incorrectly classified as mutations in other cardiac genes.3 A high degree of normal genetic variation has been demonstrated in the cardiac genes of healthy controls,4 which may, especially with missense mutations, be mistakenly interpreted as pathogenic mutations. Based on the level of evidence presented in the article, we urge caution in interpreting the RYR2 “S4153R” variant as a mutation. Some evidence does not fully support pathogenicity; bioinformatics analyses provide contradictory results, with Polymorphism Phenotype-2 (Polyphen-2) predicting probably damaging (score of 0.999) and Sort Intolerant From Tolerant (SIFT) predicting the substitution is tolerated. The importance of defining this variant lies in the genetic counselling and cardiological advice given to at-risk relatives of the proband. A better description of this variant might be “suspected pathogenic mutation.” Further evidence would be welcomed to fully support the conclusion that this variant is the cause of catecholaminergic polymorphic ventricular tachycardia in this patient. Tara L. Dzwiniel, MSc Dawna M. Gilchrist, MD, FRCPC, FCCMG Edmonton Medical Genetics Clinic University of Alberta Edmonton, Alberta, Canada
[email protected]
Edmonton Molecular Diagnostic Lab University of Alberta Edmonton, Alberta, Canada
Disclosures The authors have no conflicts of interest to disclose. References 1. Richards CS, Bale S, Bellissimo DB, et al.; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee. ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007. Genet Med 2008;10:294-300. 2. Wilde AA, Ackerman MJ. Exercise extreme caution when calling rare genetic variants novel arrhythmia syndrome susceptibility mutations. Heart Rhythm 2010;7:1883-5. 3. Gandjbakhch E, Charron P, Fressart V, et al. Plakophilin 2A is the dominant isoform in human heart tissue: consequences for the genetic screening of arrhythmogenic right ventricular cardiomyopathy. Heart 2011;97:844-9. 4. Kapplinger JD, Landstrom AP, Salisbury BA, et al. Distinguishing arrhythmogenic right ventricular cardiomyopathy/dysplasia-associated mutations from background genetic noise. J Am Coll Cardiol 2011;57:2317-27.
doi:10.1016/j.cjca.2011.10.001 Reply to Letter from Dzwiniel et al.—Making a Clinical Diagnosis of CPVT: Putting It All Together To the Editor: We thank Dzwiniel et al. for their interest in our Case Report of catecholaminergic polymorphic ventricular tachycardia (CPVT)1 and for raising the critical issue regarding the results of genetic testing. The diagnosis of CPVT is based on clinical features and family history in combination with the results of genetic testing.2 The clinical features consistent with a diagnosis of CPVT in our case included exercise/stress related syncope with documented polymorphic ventricular tachycardia and exercise-induced polymorphic extrasystoles suppressed by -blocker therapy along with a structurally normal heart and normal coronary arteries. Genetic analysis failed to show defects in cardiac sodium and potassium channels, but detected a substitution mutation resulting in an arginine substitution for serine in position 4153 of the RyR2 protein. The genetic testing involved 2 independent laboratories. The initial testing from Silvia Priori group (Molecular Cardiology Laboratories, Pavia, Italy) classified the RyR2 mutation (S4153R) as a class I mutation and “pathogenic.” To exclude
0828-282X/12/$ – see front matter © 2012 Canadian Cardiovascular Society. Published by Elsevier Inc. All rights reserved.
Letters to the Editor Stacey Hume, PhD, FCCMG
How Much Is Enough? Weighing the Evidence for Mutation Pathogenicity To the Editor: We read with great interest the recent publication by Kazemian et al. in the November/December 2011 issue. The authors report a novel missense mutation in the RYR2 gene: S4153R or A12457C (recommended Human Genome Variation Society nomenclature: p.Ser4153Arg, c.12457A⬎C). This sequence variant is in a residue conserved among mammals, in a domain II “hotspot” region of the RYR2 gene, and results in a nonsynonymous amino acid change. Therefore, one might suspect it to be disease causing, ie, a pathogenic mutation. Recommendations for the interpretation and reporting of sequence variations have been published.1 Several factors that may suggest that a variant is a deleterious mutation include cosegregation of the variant with the disease in the family, increased prevalence of the variant in cases vs healthy controls, sequence conservation between species, the nature of the amino acid substitution, and protein functional analysis.1 In this case, CASQ2 screening, family cosegregation studies, and functional analysis were not performed. Additionally, the prevalence of this variant in healthy controls has not been studied. Recently others have reported on the inherent difficulties in interpreting novel sequence variants.2-4 Variants have been incorrectly classified as mutations in other cardiac genes.3 A high degree of normal genetic variation has been demonstrated in the cardiac genes of healthy controls,4 which may, especially with missense mutations, be mistakenly interpreted as pathogenic mutations. Based on the level of evidence presented in the article, we urge caution in interpreting the RYR2 “S4153R” variant as a mutation. Some evidence does not fully support pathogenicity; bioinformatics analyses provide contradictory results, with Polymorphism Phenotype-2 (Polyphen-2) predicting probably damaging (score of 0.999) and Sort Intolerant From Tolerant (SIFT) predicting the substitution is tolerated. The importance of defining this variant lies in the genetic counselling and cardiological advice given to at-risk relatives of the proband. A better description of this variant might be “suspected pathogenic mutation.” Further evidence would be welcomed to fully support the conclusion that this variant is the cause of catecholaminergic polymorphic ventricular tachycardia in this patient. Tara L. Dzwiniel, MSc Dawna M. Gilchrist, MD, FRCPC, FCCMG Edmonton Medical Genetics Clinic University of Alberta Edmonton, Alberta, Canada
[email protected]
Edmonton Molecular Diagnostic Lab University of Alberta Edmonton, Alberta, Canada
Disclosures The authors have no conflicts of interest to disclose. References 1. Richards CS, Bale S, Bellissimo DB, et al.; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee. ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007. Genet Med 2008;10:294-300. 2. Wilde AA, Ackerman MJ. Exercise extreme caution when calling rare genetic variants novel arrhythmia syndrome susceptibility mutations. Heart Rhythm 2010;7:1883-5. 3. Gandjbakhch E, Charron P, Fressart V, et al. Plakophilin 2A is the dominant isoform in human heart tissue: consequences for the genetic screening of arrhythmogenic right ventricular cardiomyopathy. Heart 2011;97:844-9. 4. Kapplinger JD, Landstrom AP, Salisbury BA, et al. Distinguishing arrhythmogenic right ventricular cardiomyopathy/dysplasia-associated mutations from background genetic noise. J Am Coll Cardiol 2011;57:2317-27.
doi:10.1016/j.cjca.2011.10.001 Reply to Letter from Dzwiniel et al.—Making a Clinical Diagnosis of CPVT: Putting It All Together To the Editor: We thank Dzwiniel et al. for their interest in our Case Report of catecholaminergic polymorphic ventricular tachycardia (CPVT)1 and for raising the critical issue regarding the results of genetic testing. The diagnosis of CPVT is based on clinical features and family history in combination with the results of genetic testing.2 The clinical features consistent with a diagnosis of CPVT in our case included exercise/stress related syncope with documented polymorphic ventricular tachycardia and exercise-induced polymorphic extrasystoles suppressed by -blocker therapy along with a structurally normal heart and normal coronary arteries. Genetic analysis failed to show defects in cardiac sodium and potassium channels, but detected a substitution mutation resulting in an arginine substitution for serine in position 4153 of the RyR2 protein. The genetic testing involved 2 independent laboratories. The initial testing from Silvia Priori group (Molecular Cardiology Laboratories, Pavia, Italy) classified the RyR2 mutation (S4153R) as a class I mutation and “pathogenic.” To exclude
0828-282X/12/$ – see front matter © 2012 Canadian Cardiovascular Society. Published by Elsevier Inc. All rights reserved.