ClinVar Genomic variation as it relates to human health

This variant has not been identified in large population databases (Gnomad, 1000 Genomes, Go NL, Exome Variant Server) and is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. In addition, the variant has been reported previously in individuals with cardiomyopathy. Functional studies demonstrate that this variant causes abberrant phosphorylation of contractile proteins, reduced maximal force-generating capacity of cardiomyocytes, and enhanced Ca2+ sensitivity (PMID: 19273718 ).

The c.2373dupG pathogenic mutation, located in coding exon 24 of the MYBPC3 gene, results from a duplication of G at nucleotide position 2373, causing a translational frameshift with a predicted alternate stop codon (p.W792Vfs*41). This mutation has been identified in multiple unrelated individuals with hypertrophic cardiomyopathy (HCM), reported to co-segregate with disease in several families, and is published as a Dutch founder mutation (Niimura et al. N Engl J Med. 1998;338(18):1248-57 (reported as InsG791); Alders et al. Eur Heart J. 2003;24(20):1848-53; Christiaans et al. Neth Heart J. 2010;18(5):248-54 (reported as 2373_2374insG)). In the homozygous state, this mutation has been reported in a patient with neonatal lethal cardiomyopathy (Wessels MW et al. Eur. J. Hum. Genet., 2015 Jul;23:922-8). In addition, multiple functional studies have reported this mutation to result in loss of function (Moolman et al. Circulation. 2000;101(12):1396-402; van Dijk et al. Circulation. 2009;119(11):1473-83; Marston S et al. J Muscle Res Cell Motil. 2012;33(1):75-80; Wijnker PJ et al. J. Mol. Cell. Cardiol., 2016 Aug;97:82-92 (reported as 2373_2374insG)). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

PVS1, PS4

This sequence change creates a premature translational stop signal (p.Trp792Valfs*41) in the MYBPC3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MYBPC3 are known to be pathogenic (PMID: 19574547). This variant is present in population databases (rs397515963, gnomAD 0.004%). This premature translational stop signal has been observed in individuals with hypertrophic cardiomyopathy (HCM) or neonatal cardiomyopathy with features of left ventricular non-compaction and septal defects (PMID: 9562578, 10736283, 19273718, 22115648, 22574137, 25335496). It is commonly reported in individuals of Dutch ancestry (PMID: 14563344, 20505798). ClinVar contains an entry for this variant (Variation ID: 42619). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. For these reasons, this variant has been classified as Pathogenic.

The p.Trp792ValfsX41 variant in MYBPC3 has been reported in multiple individuals with hypertrophic cardiomyopathy (HCM) and has shown strong segregation with disease in multiple families (Niimura 1998 PMID: 9562578, Moolman 2000 PMID: 10736283, Maron 2001 PMID: 11499718, Ortlepp 2002 PMID: 11847170, Alders 2003 PMID: 14563344, Walsh 2017 PMID: 27532257, LMM data). This variant a likely Dutch founder variant and is estimated to account for approximately 25% of cases of HCM in the Netherlands (Alders 2003 PMID: 14563344). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 42619) and has been identified in 0.004% (3/70142) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). Please note that for diseases with clinical variability and incomplete or age-dependent penetrance, pathogenic variants may be present at a low frequency in the general population. This variant is predicted to cause a frameshift, which alters the protein’s amino acid sequence beginning at position 792 and leads to a premature termination codon 41 amino acids downstream. This alteration is then predicted to lead to a truncated or absent protein. In vitro functional studies support that this variant leads to a loss-of-function (Moolman 2000 PMID: 10736283). Heterozygous loss of function of the MYBPC3 gene is an established disease mechanism in autosomal dominant HCM. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant HCM. ACMG/AMP Criteria applied: PVS1, PS4, PP1_Strong, PM2_Supporting.

ACMG score pathogenic

Variant summary: The MYBPC3 c.2373dupG (p.Trp792ValfsX41) variant results in a premature termination codon, predicted to cause a truncated or absent MYBPC3 protein due to nonsense mediated decay, which are commonly known mechanisms for disease. A functional study, Van Dijk_2009, supports this variant causing loss-of-function. This variant was found in 3/166724 control chromosomes (gnomAD) at a frequency of 0.000018, which does not exceed the estimated maximal expected allele frequency of a pathogenic MYBPC3 variant (0.0010005). Multiple publications have cited the variant in affected individuals, predominantly of Dutch origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic.

This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PVS1,PS3,PP3.

This sequence change results in a frameshift variant in the MYBPC3 gene (p.(Trp792ValFs*41)) resulting in loss-of function and haploinsufficiency, which is a known disease mechanism(PVS1) (PMID: 19273718). This variant is present in population databases (GnomAD 3/166724). This variant has been reported in the literature in several families with HCM and showed co-seggregation with HCM (PP1strong) (PMID:9562578; PMID: 10736283; PMID: 14563344; PMID: 19356534; PMID: 23674513; PMID: 24111713; PMID: 27476098; PMID:25335496).It has been described as a Dutch Founder variant, present in 17-25% of all HCM cases (PS4) (PMID: 20505798, 14563344).Functional studies demonstrated that the variant reduced maximal force-generating capacity of cardiomyocytes(PS3) (PMID: 19273718). We identified this variant in two HCM families. In conclusion this variant was classified as a pathogenic variant according to ACMG-guidelines (PVS1; PP1strong; PS4;PS3).

PVS1, PS4, PP5

_x000D_reported as incidental finding according to ACMG Criteria applied: PVS1, PS4

The MYBPC3 c.2373dup; p.Trp792ValfsTer41 variant (rs397515963), also known as 2373insG or InsG791, is reported in the literature as a pathogenic founder variant associated with hypertrophic cardiomyopathy (HCM), particularly in individuals of Dutch ancestry (Alders 2003, Moolman 2000, Nannenberg 2011, Niimura 1998). This variant has been reported to segregate with disease with incomplete penetrance in multiple large families affected with HCM (Alders 2003, Moolman 2000, Nannenberg 2011, Niimura 1998). This variant is reported as pathogenic by multiple laboratories in ClinVar (Variation ID: 42619) and is found in the general population with a low overall allele frequency of 0.002% (3/172018 alleles) in the Genome Aggregation Database. This variant causes a frameshift by inserting a single nucleotide, so it is predicted to result in a truncated protein or mRNA subject to nonsense-mediated decay. Computational analyses (Alamut v.2.11) also predict that this variant may impact splicing by creating a novel cryptic donor splice site, and functional analyses of the variant protein show use of the cryptic splice site, leading to a frameshift and haploinsufficiency (Moolman 2000, van Dijk 2009). Based on available information, the c.2373dup variant is considered to be pathogenic. References: Alders M et al. The 2373insG mutation in the MYBPC3 gene is a founder mutation, which accounts for nearly one-fourth of the HCM cases in the Netherlands. Eur Heart J. 2003 Oct;24(20):1848-53. PMID: 14563344 Moolman JA et al. A newly created splice donor site in exon 25 of the MyBP-C gene is responsible for inherited hypertrophic cardiomyopathy with incomplete disease penetrance. Circulation. 2000 Mar 28;101(12):1396-402. PMID: 10736283. Nannenberg EA et al. Mortality risk of untreated myosin-binding protein C-related hypertrophic cardiomyopathy: insight into the natural history. J Am Coll Cardiol. 2011 Nov 29;58(23):2406-14. PMID: 22115648 Niimura H et al. Mutations in the gene for cardiac myosin-binding protein C and late-onset familial hypertrophic cardiomyopathy. N Engl J Med. 1998 Apr 30;338(18):1248-57. PMID: 9562578. van Dijk SJ et al. Cardiac myosin-binding protein C mutations and hypertrophic cardiomyopathy: haploinsufficiency, deranged phosphorylation, and cardiomyocyte dysfunction. Circulation. 2009 Mar 24;119(11):1473-83. PMID: 19273718

Observed in individuals with severe infantile-onset cardiomyopathy who were either homozygous for this variant or compound heterozygous for this variant and a second pathogenic variant in the MYBPC3 gene (Lekanne Deprez et al., 2006; Haberer et al., 2014; Wessels et al., 2015); Not observed at significant frequency in large population cohorts (gnomAD); Published functional studies demonstrate c.2373dupG causes haploinsufficiency, deranged phosphorylation of contractile proteins, reduced maximal force-generating capacity of cardiomyocytes, and enhanced Ca2+ sensitivity (van Dijk et al., 2009); Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 30731207, 29759671, 23674513, 22569109, 20705073, 27532257, 28615295, 28005231, 20505798, 24111713, 19356534, 19666645, 25262865, 23396983, 23074333, 26489474, 21257752, 22115648, 9562578, 27476098, 22173300, 24510615, 16679492, 25335496, 28794111, 22574137, 29540445, 28971120, 29169752, 30025578, 29237689, 28790153, 19574547, 29212898, 26914223, 29447731, 29121657, 27108529, 30775854, 30742251, 31006259, 30550750, 31737537, 32880476, 14563344, 32686758, 32746448, 19273718, 31513939, 33849460, 33662488, 33673806, 30847666, 34135346, 33726816, 33087929)

This variant inserts 1 nucleotide in exon 24 of the fibronectin type 3 domain C6 of the MYBPC3 gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. RNA studies have shown that this variant creates a new splice donor site, which could also result in a frameshift and premature truncation (PMID: 10736283). This variant has been reported in over 300 individuals affected with hypertrophic cardiomyopathy (PMID: 9562578, 14563344, 19273718, 20505798, 22115648, 22574137, 35653365) and occurs in up to 25% of Dutch individuals affected with hypertrophic cardiomyopathy (PMID: 14563344, 20505798). A study of a large multigenerational family affected with hypertrophic cardiomyopathy has shown that penetrance of this variant is incomplete and age-dependent (PMID: 10736283). This variant has also been reported in an individual affected with dilated cardiomyopathy (PMID: 32880476), and it has also been reported in compound heterozygous or homozygous state in three Dutch neonates with lethal cardiomyopathy (PMID: 25335496). This variant has been identified in 3/172018 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of MYBPC3 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.

MYBPC3: PVS1, PP1:Strong, PM2, PS4:Moderate, PS3:Supporting

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with dilated cardiomyopathy 1MM (MIM#615396), hypertrophic cardiomyopathy 4 (MIM#115197) and left ventricular noncompaction 10 (MIM#615396) (OMIM). (I) 0108 - This gene is associated with both recessive and dominant disease. Heterozygous variants are frequently reported in adult onset conditions, however recessive inheritance results in a more severe early onset phenotype (OMIM). (I) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction). (SP) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (3 heterozygotes, 0 homozygotes). (SP) 0701 - Other NMD-predicted variants comparable to the one identified in this case have very strong previous evidence for pathogenicity. Many other NMD-predicted variants have previously been classified as pathogenic (ClinVar). (SP) 0801 - Very strong previous evidence of pathogenicity in unrelated individuals. The variant has previously been reported as pathogenic in multiple affected individuals with hypertrophic cardiomyopathy and is considered to be a founder mutation in the Dutch population (PMIDs: 14563344, 32009526, 32841044, ClinVar). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Mutant constructs expressed in mouse MYBPC3 KO engineered heart tissues displayed significantly different maximal force, contraction and relaxation kinetics, and external Ca2+ sensitivities compared with WT constructs. Moreover, mutant constructs were unable to rescue the MYBPC3 KO phenotype when expressed in either homozygous and heterozygous states (PMID: 27108529). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

PP1_very_strong, PM2, PS3, PS4, PVS1

This variant inserts 1 nucleotide in exon 24 of the fibronectin type 3 domain C6 of the MYBPC3 gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. RNA studies has shown that this variant may create a new splice donor site, which could also result in a frameshift and premature truncation (PMID: 10736283). This variant has been reported in over 300 individuals affected with hypertrophic cardiomyopathy (PMID: 9562578, 14563344, 19273718, 20505798, 22115648, 22574137, 35653365) and occurs in up to 25% of Dutch individuals affected with hypertrophic cardiomyopathy (PMID: 14563344, 20505798). A study of a large multigenerational family affected with hypertrophic cardiomyopathy has shown that penetrance of this variant is incomplete and age-dependent (PMID: 10736283). This variant has also been reported in an individual affected with dilated cardiomyopathy (PMID: 32880476), and it has also been reported in compound heterozygous or homozygous state in three Dutch neonates with lethal cardiomyopathy (PMID: 25335496). This variant has been identified in 3/172018 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of MYBPC3 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.

Note this variant was found in clinical genetic testing performed by one or more labs who may also submit to ClinVar. Thus any internal case data may overlap with the internal case data of other labs. The interpretation reviewed below is that of the Stanford Center for Inherited Cardiovascular Disease. p.Trp792ValfsX41 (c.2373dupG) in MYBPC3. Based on the data reviewed below we consider this variant very likely disease-causing. This variant is in exon 24 of the MYBPC3 gene. The c.2373dupG variant causes a shift in the reading frame beginning with Tryptophan residue 792 changing to a Valine and creating a premature stop codon at position 41 of the new reading frame. It is expected to results in an abnormal, truncated protein or in absence of protein due to mRNA decay. Nonsense and splicing variants are frequently seen in MYBPC3 in association with cardiomyopathy. To the best of our knowledge no experimental studies have demonstrated impact on splicing or the final protein product. Moolman et al (2000) were not able to identify a truncated protein product using immunohistochemistry. In total this variant has been observed in at least ~14 unrelated individuals with HCM, though three of those cases were shown to share a common founder. We have seen it in 6 families with HCM, including this patient’s family (as of October 29, 2014). Nimura et al (1998) reported this variant in 3 families with HCM. In those families 115 individuals were genotype positive for the variant; of these 45 individuals were phenotype positive for HCM. There were 10 reported disease related deaths among this group. Haplotype analysis indicated that this was a founder mutation in these 3 families. Moolman et al (2000) also described a family with HCM with this variant. A family of 49 individuals was analyzed in this publication, out of these 27 were found to be genotype positive for the variant – 10 individuals fulfilled the diagnostic criteria for HCM, 5 individuals were borderline for the disease, 12 had normal echo/ecgs and no symptoms, 2 individuals required a myectomy and 2 individuals experienced a SCD event. Alders et al (2003) reported that this variant is common in HCM patients in the Netherlands. GeneDx also reports this variant has been seen in multiple unrelated individuals tested for HCM at their laboratory(many of whom likely include our patients). This variant has been reported in multiple additional cases of HCM and (Maron et al 2001; Ortlepp et al 2002; Waldmuller et al 2002; Richard et al 2003; Van Driest et al 2004; Barr et al 2001).Some authors have suggested that this variant is associated with later onset of disease. In the kindred reported by Moolman et al (200), age of onset was late in life (often after than 30 yrs old), and Kaplan Meier survival curve illustrated near normal survival at age 50 (95%). In total the variant has not been seen in 7,200 laboratory controls, published controls and individuals from publicly available population datasets. There is no variation at codon 792 listed in the NHLBI Exome Sequencing Project dataset, which currently includes variant calls on ~6,500 Caucasian and African American individuals (as of 10/15/14). There is also no variation at this codon listed in dbSNP or 1000 genomes (as of 10/15/13). The variant was not observed in the following laboratory and published control samples: Van Driest et al (2004) did not observe the variant in 200 presumably healthy controls of unknown ancestry. Based on literature review it is unclear if the control populations used in the Niimura and Moolman publications are the same or if they represent 2 distinct groups of normal individuals-each report 100 controls. Review of a Familion/PGX testing report on the variant indicates that they did not find the variant in 400 presumably healthy control individuals (July 2009).

MYBPC3 Trp792fs has been well described in multiple families and individuals with HCM (see literature). It is one of three main founder mutations in MYBPC3 in HCM patients in the Netherlands (Alders M, et al., 2003; Christianns I, et al., 2010). This Trp792fs mutation accounts for nearly 25% of all HCM cases in the Netherlands (Alders M, et al., 2003). Familial segregation (where available) shows evidence of co-segregation (Niimura H, et al., 1998; Moolman JA, et al., 2000; Maron BJ, et al., 2001). The variant is present at a low frequency in the Genome Aggregation Database (http://gnomad.broadinstitute.org/). We have identified this MYBPC3 Trp792fs mutation in 12 unrelated HCM probands and the variant has been found to segregate with disease in several of our families. Based on the adapted ACMG guidelines (Kelly MA, et al., 2018), this variant results in loss of function of MYBPC3 (PVS1), has been identified in well over 15 HCM probands (PS4), segregates strongly with disease (PP1_strong) and is rare in the general population (PM2), therefore we classify MYBPC3 Trp792fs as 'pathogenic'.

The MYBPC3 c.2373dupG variant is predicted to result in a frameshift and premature protein termination (p.Trp792Valfs*41). This variant has been reported in multiple unrelated individuals with hypertrophic cardiomyopathy (Niimura et al. 1998. PubMed ID: 9562578) and has been described as a founder variant in the Dutch population (Christiaans et al. 2010. PubMed ID: 20505798). This variant is reported in 0.0043% of alleles in individuals of European (Non-Finnish) descent in gnomAD and interpreted as pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/42619/). Frameshift variants in MYBPC3 are expected to be pathogenic. This variant is interpreted as pathogenic.

Variant interpreted as Pathogenic and reported on 11-17-2017 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.