scholarly journals Computational prediction of protein subdomain stability in MYBPC3 enables clinical risk stratification in hypertrophic cardiomyopathy and enhances variant interpretation

2021 ◽  
Author(s):  
Andrea D. Thompson ◽  
Adam S. Helms ◽  
Anamika Kannan ◽  
Jaime Yob ◽  
Neal K. Lakdawala ◽  
...  
Keyword(s):  
Hypertrophic Cardiomyopathy ◽  
Composite Endpoint ◽  
Computational Prediction ◽  
Saturation Mutagenesis ◽  
Event Analysis ◽  
Loss Of Function ◽  
Missense Variants ◽  
Clinical Risk ◽  
Number Of Patients ◽  
Uncertain Significance

Abstract Purpose Variants in MYBPC3 causing loss of function are the most common cause of hypertrophic cardiomyopathy (HCM). However, a substantial number of patients carry missense variants of uncertain significance (VUS) in MYBPC3. We hypothesize that a structural-based algorithm, STRUM, which estimates the effect of missense variants on protein folding, will identify a subgroup of HCM patients with a MYBPC3 VUS associated with increased clinical risk. Methods Among 7,963 patients in the multicenter Sarcomeric Human Cardiomyopathy Registry (SHaRe), 120 unique missense VUS in MYBPC3 were identified. Variants were evaluated for their effect on subdomain folding and a stratified time-to-event analysis for an overall composite endpoint (first occurrence of ventricular arrhythmia, heart failure, all-cause mortality, atrial fibrillation, and stroke) was performed for patients with HCM and a MYBPC3 missense VUS. Results We demonstrated that patients carrying a MYBPC3 VUS predicted to cause subdomain misfolding (STRUM+, ΔΔG ≤ −1.2 kcal/mol) exhibited a higher rate of adverse events compared with those with a STRUM- VUS (hazard ratio = 2.29, P = 0.0282). In silico saturation mutagenesis of MYBPC3 identified 4,943/23,427 (21%) missense variants that were predicted to cause subdomain misfolding. Conclusion STRUM identifies patients with HCM and a MYBPC3 VUS who may be at higher clinical risk and provides supportive evidence for pathogenicity.

scholarly journals Computational prediction of protein subdomain stability in MYBPC3 enables clinical risk stratification in hypertrophic cardiomyopathy and enhances variant interpretation

2020 ◽  
Author(s):  
Andrea D. Thompson ◽  
Adam S. Helms ◽  
Anamika Kannan ◽  
Jaime Yob ◽  
Neal K. Lakdawala ◽  
...  
Keyword(s):  
Risk Stratification ◽  
Clinical Decision Making ◽  
Composite Endpoint ◽  
Computational Prediction ◽  
Saturation Mutagenesis ◽  
Event Analysis ◽  
Loss Of Function ◽  
Missense Variants ◽  
Clinical Risk ◽  
Number Of Patients

AbstractPurposeVariants in MYBPC3 causing loss-of-function are the most common cause of HCM. However, a substantial number of patients carry missense variants of uncertain significance (VUS) in MYBPC3. We hypothesize that a structural-based algorithm, STRUM, which estimates the effect of missense variants on protein folding, will improve clinical risk stratification of patients with HCM and a MYBPC3 VUS.MethodsAmong 7,963 patients in the multi-center Sarcomeric Human Cardiomyopathy Registry, 120 unique missense VUSs in MYBPC3 were identified. Variants were evaluated for their effect on subdomain folding and a stratified time-to-event analysis for an overall composite endpoint (first occurrence of ventricular arrhythmia, heart failure, all-cause mortality, atrial fibrillation, and stroke) was performed for patients with HCM and a MYBPC3 missense VUS.ResultsWe demonstrated that patients carrying a MYBPC3 VUS predicted to cause subdomain misfolding (STRUM +, ΔΔG ≤-1.2 kcal/mol) exhibited a higher rate of adverse events compared to those with a STRUM-VUS (Hazard Ratio=2.29, P=0.0282). In silico saturation mutagenesis of MYBPC3 identified 4,943/23,427 (21%) missense variants that were predicted to cause subdomain misfolding.ConclusionsSTRUM enables clinical risk stratification of patients with HCM and a MYBPC3 VUS and has the capacity to improve prognostic predictions and clinical decision making.

Abstract 14781: Computational Prediction of Protein Subdomain Stability as a Novel Approach to Cardiac Myosin Binding ProteinC Variant Adjudication and Clinical Risk Stratification in Hypertrophic Cardiomyopathy

Circulation ◽  
2020 ◽  
Vol 142 (Suppl_3) ◽  
Author(s):  
Andrea D Thompson ◽  
Adam S Helms ◽  
Anamika Kannan ◽  
Jaime Yob ◽  
Neal K Lakdawala ◽  
...  
Keyword(s):  
Risk Stratification ◽  
Clinical Decision Making ◽  
Saturation Mutagenesis ◽  
Event Analysis ◽  
Cardiac Myosin ◽  
Loss Of Function ◽  
Missense Variants ◽  
Clinical Risk ◽  
Number Of Patients ◽  
Myosin Binding

Introduction: Patients with HCM and a pathogenic sarcomere variant have a higher risk of adverse clinical outcomes compared to those without a sarcomere gene variant. Pathogenic truncating variants in MYBPC3 (encoding cardiac myosin binding protein C, MYBP-C) cause loss-of-function and are the most common genetic cause of HCM. However, a substantial number of patients carry missense variants in MYBPC3 that cannot be clearly classified as either pathogenic or benign. Interpretation of these variants of uncertain significance (VUS) remain a significant challenge. Hypothesis: We hypothesize that a structural-based algorithm, STRUM, which estimates the effect of missense variants on subdomain protein folding, will enable clinical risk stratification of patients with HCM and a MYBPC3 VUS. Methods and Results: Among the 7,963 patients in the multi-center Sarcomeric Human Cardiomyopathy Registry (SHaRe), 19 unique missense pathogenic variants and 120 missense VUSs in MYBPC3 were identified. Within SHaRe and GnomAD, 110 benign missense variants (allele frequency > 4e-05) were identified. Following structural modeling of each MyBP-C domain, variants were predicted to cause subdomain misfolding if ΔΔG < = -1.2 kcal/mol (STRUM+). 93% of benign variants were predicted to be STRUM (-). Time-event analysis for an overall composite clinical endpoint [defined as the first occurrence of ventricular arrhythmia, heart failure, all-cause mortality, atrial fibrillation (AF), or stroke] demonstrated that patients carrying a STRUM+ MYBPC3 VUS exhibited a higher rate of adverse events compared to those with a STRUM- VUS (Hazard Ratio=2.29, P=0.0282). Of the 120 missense VUSs, 34 (28%) were STRUM+. In silico saturation mutagenesis of MYBPC3 identified 4,943/23,427 (21%) missense variants predicted to cause subdomain misfolding. Conclusions: STRUM is capable of clinically risk stratifying HCM patients with a MYBPC3 VUSs . These findings support the routine use of STRUM in variant interpretation algorithms and clinical decision making.

scholarly journals Massively parallel functional testing of MSH2 missense variants conferring Lynch Syndrome risk

2020 ◽  
Author(s):  
Xiaoyan Jia ◽  
Bala Bharathi Burugula ◽  
Victor Chen ◽  
Rosemary M. Lemons ◽  
Sajini Jayakody ◽  
...  
Keyword(s):  
Lynch Syndrome ◽  
Massively Parallel ◽  
Loss Of Function ◽  
Missense Variants ◽  
Dna Mismatch ◽  
Uncertain Significance ◽  
Repair Factor ◽  
Key Barrier ◽  
Cancer Syndromes

AbstractThe lack of functional evidence for the majority of missense variants limits their clinical interpretability, and poses a key barrier to the broad utility of carrier screening. In Lynch Syndrome (LS), one of the most highly prevalent cancer syndromes, nearly 90% of clinically observed missense variants are deemed “variants of uncertain significance” (VUS). To systematically resolve their functional status, we performed a massively parallel screen in human cells to identify loss-of-function missense variants in the key DNA mismatch repair factor MSH2. The resulting functional effect map is substantially complete, covering 94% of the 17,746 possible variants, and is highly concordant (96%) with existing functional data and expert clinicians’ interpretations. The large majority (89%) of missense variants were functionally neutral, perhaps unexpectedly in light of its evolutionary conservation. These data provide ready-to-use functional evidence to resolve the ∼1,300 extant missense VUSs in MSH2, and may facilitate the prospective classification of newly discovered variants in the clinic.

scholarly journals Spatial and Functional Distribution of MYBPC3 Pathogenic Variants and Clinical Outcomes in Patients With Hypertrophic Cardiomyopathy

2020 ◽  
Vol 13 (5) ◽  
pp. 396-405 ◽  
Author(s):  
Adam S. Helms ◽  
Andrea D. Thompson ◽  
Amelia A. Glazier ◽  
Neha Hafeez ◽  
Samat Kabani ◽  
...  
Keyword(s):  
Hypertrophic Cardiomyopathy ◽  
Clinical Outcomes ◽  
Left Ventricular ◽  
Familial Hypertrophic Cardiomyopathy ◽  
Clinical Severity ◽  
Event Analysis ◽  
Loss Of Function ◽  
Class Iii ◽  
Pathogenic Variants ◽  
Degradation Rates

Background: Pathogenic variants in MYBPC3 , encoding cardiac MyBP-C (myosin binding protein C), are the most common cause of familial hypertrophic cardiomyopathy. A large number of unique MYBPC3 variants and relatively small genotyped hypertrophic cardiomyopathy cohorts have precluded detailed genotype-phenotype correlations. Methods: Patients with hypertrophic cardiomyopathy and MYBPC3 variants were identified from the Sarcomeric Human Cardiomyopathy Registry. Variant types and locations were analyzed, morphological severity was assessed, and time-event analysis was performed (composite clinical outcome of sudden death, class III/IV heart failure, left ventricular assist device/transplant, atrial fibrillation). For selected missense variants falling in enriched domains, myofilament localization and degradation rates were measured in vitro. Results: Among 4756 genotyped patients with hypertrophic cardiomyopathy in Sarcomeric Human Cardiomyopathy Registry, 1316 patients were identified with adjudicated pathogenic truncating (N=234 unique variants, 1047 patients) or nontruncating (N=22 unique variants, 191 patients) variants in MYBPC3 . Truncating variants were evenly dispersed throughout the gene, and hypertrophy severity and outcomes were not associated with variant location (grouped by 5′–3′ quartiles or by founder variant subgroup). Nontruncating pathogenic variants clustered in the C3, C6, and C10 domains (18 of 22, 82%, P <0.001 versus Genome Aggregation Database common variants) and were associated with similar hypertrophy severity and adverse event rates as observed with truncating variants. MyBP-C with variants in the C3, C6, and C10 domains was expressed in rat ventricular myocytes. C10 mutant MyBP-C failed to incorporate into myofilaments and degradation rates were accelerated by ≈90%, while C3 and C6 mutant MyBP-C incorporated normally with degradation rate similar to wild-type. Conclusions: Truncating variants account for 91% of MYBPC3 pathogenic variants and cause similar clinical severity and outcomes regardless of location, consistent with locus-independent loss-of-function. Nontruncating MYBPC3 pathogenic variants are regionally clustered, and a subset also cause loss of function through failure of myofilament incorporation and rapid degradation. Cardiac morphology and clinical outcomes are similar in patients with truncating versus nontruncating variants.

scholarly journals Hemi- and Homozygous Loss-of-Function Mutations in DSG2 (Desmoglein-2) Cause Recessive Arrhythmogenic Cardiomyopathy with an Early Onset

2021 ◽  
Vol 22 (7) ◽  
pp. 3786
Author(s):  
Andreas Brodehl ◽  
Alexey Meshkov ◽  
Roman Myasnikov ◽  
Anna Kiseleva ◽  
Olga Kulikova ◽  
...  
Keyword(s):  
Medical History ◽  
Splice Site Mutation ◽  
Pathogenic Mutation ◽  
Large Deletion ◽  
Loss Of Function ◽  
Arrhythmogenic Cardiomyopathy ◽  
Site Mutation ◽  
Snp Arrays ◽  
Number Of Patients ◽  
History Of

About 50% of patients with arrhythmogenic cardiomyopathy (ACM) carry a pathogenic or likely pathogenic mutation in the desmosomal genes. However, there is a significant number of patients without positive familial anamnesis. Therefore, the molecular reasons for ACM in these patients are frequently unknown and a genetic contribution might be underestimated. Here, we used a next-generation sequencing (NGS) approach and in addition single nucleotide polymor-phism (SNP) arrays for the genetic analysis of two independent index patients without familial medical history. Of note, this genetic strategy revealed a homozygous splice site mutation (DSG2–c.378+1G>T) in the first patient and a nonsense mutation (DSG2–p.L772X) in combination with a large deletion in DSG2 in the second one. In conclusion, a recessive inheritance pattern is likely for both cases, which might contribute to the hidden medical history in both families. This is the first report about these novel loss-of-function mutations in DSG2 that have not been previously identi-fied. Therefore, we suggest performing deep genetic analyses using NGS in combination with SNP arrays also for ACM index patients without obvious familial medical history. In the future, this finding might has relevance for the genetic counseling of similar cases.

scholarly journals Loss-of-function and missense variants in NSD2 cause decreased methylation activity and are associated with a distinct developmental phenotype

2021 ◽  
Author(s):  
Paolo Zanoni ◽  
Katharina Steindl ◽  
Deepanwita Sengupta ◽  
Pascal Joset ◽  
Angela Bahr ◽  
...  
Keyword(s):  
Loss Of Function ◽  
Mild Phenotype ◽  
Psychological Issues ◽  
Missense Variants ◽  
Mild Developmental Delay ◽  
Pathogenic Variants ◽  
In Silico Modeling ◽  
And Function ◽  
Methylation Activity

Abstract Purpose Despite a few recent reports of patients harboring truncating variants in NSD2, a gene considered critical for the Wolf–Hirschhorn syndrome (WHS) phenotype, the clinical spectrum associated with NSD2 pathogenic variants remains poorly understood. Methods We collected a comprehensive series of 18 unpublished patients carrying heterozygous missense, elongating, or truncating NSD2 variants; compared their clinical data to the typical WHS phenotype after pooling them with ten previously described patients; and assessed the underlying molecular mechanism by structural modeling and measuring methylation activity in vitro. Results The core NSD2-associated phenotype includes mostly mild developmental delay, prenatal-onset growth retardation, low body mass index, and characteristic facial features distinct from WHS. Patients carrying missense variants were significantly taller and had more frequent behavioral/psychological issues compared with those harboring truncating variants. Structural in silico modeling suggested interference with NSD2’s folding and function for all missense variants in known structures. In vitro testing showed reduced methylation activity and failure to reconstitute H3K36me2 in NSD2 knockout cells for most missense variants. Conclusion NSD2 loss-of-function variants lead to a distinct, rather mild phenotype partially overlapping with WHS. To avoid confusion for patients, NSD2 deficiency may be named Rauch–Steindl syndrome after the delineators of this phenotype.

CDK19-related disorder results from both loss-of-function and gain-of-function de novo missense variants

2021 ◽  
Author(s):  
Yuri A. Zarate ◽  
Tomoko Uehara ◽  
Kota Abe ◽  
Masayuki Oginuma ◽  
Sora Harako ◽  
...  
Keyword(s):  
De Novo ◽  
Loss Of Function ◽  
Gain Of Function ◽  
Related Disorder ◽  
Missense Variants

BDV-syndrome: An emerging syndrome with profound obesity and neurodevelopmental delay resembling Prader-Willi syndrome

2021 ◽  
Author(s):  
Elisabeth Bosch ◽  
Moritz Hebebrand ◽  
Bernt Popp ◽  
Theresa Penger ◽  
Bettina Behring ◽  
...  
Keyword(s):  
Clinical Features ◽  
Large Scale ◽  
Hypogonadotropic Hypogonadism ◽  
Computational Modelling ◽  
Prader Willi Syndrome ◽  
Loss Of Function ◽  
Human Phenotype ◽  
Neurodevelopmental Delay ◽  
Missense Variants ◽  
Severely Obese

Abstract Context CPE encodes carboxypeptidase E, an enzyme which converts proneuropeptides and propeptide hormones to bioactive forms. It is widely expressed in the endocrine and central nervous system. To date, four individuals from two families with core clinical features including morbid obesity, neurodevelopmental delay and hypogonadotropic hypogonadism, harbouring biallelic loss-of-function CPE variants, were reported. Objective We describe four affected individuals from three unrelated consanguineous families, two siblings of Syrian, one of Egyptian and one of Pakistani descent, all harbouring novel homozygous CPE loss-of-function variants. Methods After excluding Prader-Willi syndrome, exome sequencing was performed in both Syrian siblings. The variants identified in the other two individuals were reported as research variants in a large scale exome study and in ClinVar database. Computational modelling of all possible missense alterations allowed assessing CPE tolerance to missense variants. Results All affected individuals were severely obese with neurodevelopmental delay and other endocrine anomalies. Three individuals from two families shared the same CPE homozygous truncating variant c.361C&gt;T, p.(Arg121*), while the fourth carried the c.994del, p.(Ser333Alafs*22) variant. Comparison of clinical features with previously described cases and standardization according to the Human Phenotype Ontology indicated a recognisable clinical phenotype, which we termed Blakemore-Durmaz-Vasileiou (BDV) syndrome. Computational analysis indicated high conservation of CPE domains and intolerance to missense changes. Conclusions Biallelic truncating CPE variants are associated with BDV syndrome, a clinically recognisable monogenic recessive syndrome with childhood-onset obesity, neurodevelopmental delay, hypogonadotropic hypogonadism and hypothyroidism. BDV syndrome resembles Prader-Willi syndrome. Our findings suggested that missense variants may also be clinically relevant.

scholarly journals Incidental germline findings during molecular profiling of tumor tissues for precision oncology: molecular survey and methodological obstacles

2022 ◽  
Vol 20 (1) ◽  
Author(s):  
Alexandra Lebedeva ◽  
Yulia Shaykhutdinova ◽  
Daria Seriak ◽  
Ekaterina Ignatova ◽  
Ekaterina Rozhavskaya ◽  
...  
Keyword(s):  
Normal Tissue ◽  
Sanger Sequencing ◽  
Computational Prediction ◽  
Bioinformatic Analysis ◽  
Molecular Profiling ◽  
Precision Oncology ◽  
Germline Variants ◽  
Manual Curation ◽  
Uncertain Significance ◽  
Tumor Types

Abstract Background A fraction of patients referred for complex molecular profiling of biopsied tumors may harbor germline variants in genes associated with the development of hereditary cancer syndromes (HCS). Neither the bioinformatic analysis nor the reporting of such incidental germline findings are standardized. Methods Data from Next-Generation Sequencing (NGS) of biopsied tumor samples referred for complex molecular profiling were analyzed for germline variants in HCS-associated genes. Analysis of variant origin was performed employing bioinformatic algorithms followed by manual curation. When possible, the origin of the variant was validated by Sanger sequencing of the sample of normal tissue. The variants’ pathogenicity was assessed according to ACMG/AMP. Results Tumors were sampled from 183 patients (Males: 75 [41.0%]; Females: 108 [59.0%]; mean [SD] age, 57.7 [13.3] years) and analysed by targeted NGS. The most common tumor types were colorectal (19%), pancreatic (13%), and lung cancer (10%). A total of 56 sequence variants in genes associated with HCS were detected in 40 patients. Of them, 17 variants found in 14 patients were predicted to be of germline origin, with 6 variants interpreted as pathogenic (PV) or likely pathogenic (LPV), and 9 as variants of uncertain significance (VUS). For the 41 out of 42 (97%) missense variants in HCS-associated genes, the results of computational prediction of variant origin were concordant with that of experimental examination. We estimate that Sanger sequencing of a sample of normal tissue would be required for ~ 1–7% of the total assessed cases with PV or LPV, when necessity to follow with genetic counselling referral in ~ 2–15% of total assessed cases (PV, LPV or VUS found in HCS genes). Conclusion Incidental findings of pathogenic germline variants are common in data from cancer patients referred for complex molecular profiling. We propose an algorithm for the management of patients with newly detected variants in genes associated with HCS.

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