NM_000256.3(MYBPC3):c.1505G>A (p.Arg502Gln) - This variant has been reported in numerous individuals with HCM (statistically increased in individuals with cardiomyopathy compared to controls [OR lower 95% CI >20]), and shown to segregate with disease in numerous individuals across multiple families (PMIDs: 9562578, 16566405, 16858239, 18403758, 18533079, 18803133, 18957093, 20433692, 21239446, 22112859, 22857948, 23074333, 24093860, 27532257, 27561770, 27930701, LMM data, OMGL data). Therefore, the PS4 and PP1_Strong criteria have been applied. This variant is absent from gnomAD v2.1.1 (PM2_Supporting; http://gnomad.broadinstitute.org). Another variant involving this codon (p.Arg502Trp) has been identified in individuals with HCM and is classified as pathogenic by this VCEP (PM5). This variant lies in a region of the protein where variants are statistically more likely to be disease-associated with HCM (PMID: 30696458), but this cannot be combined with PM5. Computational prediction tools are inconclusive about the potential impact of this variant (REVEL score <0.7). In summary, this variant is classified as Pathogenic for HCM in an autosomal dominant manner based on PS4, PP1_Strong, PM5, and PM2_Supporting.

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 20298698, 15115610, 20378854, 32952175, 34097875, 34060810, 16715312, 31918855, 27532257, 18803133, 25342278, 22386539, 27600940, 26507537, 26183555, 25892673, 18957093, 22857948, 24093860, 24510615, 20433692, 22112859, 18403758, 16566405, 16858239, 18533079, 17224687, 22267749, 30645170, 29687901, 20738943, 29907873, 28166811, 21310275, 28193612, 31006259, 31447099, 30847666, 33658040, 9562578, 31589614, 12106841, 33407484, 34400558, 35208637, 36243179, 36264615, 36252119, 36136372, 35653365, 12707239)

The p.Arg502Gln variant in MYBPC3 has been identified in at least 15 individuals with HCM and segregated with disease in 8 affected relatives from 3 families (N iimura 1998, Olivotto 2008, Rodriguez-Garcia 2010, Otsuka 2012, LMM data). It ha s also been reported by other clinical laboratories in ClinVar (Variation ID 425 41) and was absent from large population studies. Another missense variant in t he same codon (p.Arg502Trp) is one of the most common pathogenic MYBPC3 variants associated with HCM, supporting that this codon is critical for MYBPC3 protein function. In summary, this variant meets criteria to be classified as pathogenic for HCM in an autosomal dominant manner based upon presence in multiple affecte d individuals, segregation studies, absence from the general population, and occ urrence in a critical codon. ACMG/AMP criteria applied (Richards 2015): PS4, PP1 _Strong, PM5, PM2.

Variant summary: MYBPC3 c.1505G>A (p.Arg502Gln) results in a conservative amino acid change located in the immunoglobulin subtype 2 domain (IPR003598) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 250000 control chromosomes (gnomAD and publications). c.1505G>A has been reported in the literature in many individuals affected with Hypertrophic Cardiomyopathy (HCM), including in several unrelated families where it primarily segregated with the disease phenotype (e.g. Niimura_1998, Girolami_2006, Miller_2007, Morita_2008, Rodriguez-Garcia_2010, Otsuka_2012, Walsh_2017). These data indicate that the variant is very likely to be associated with disease. A variant affecting the same codon, p.Arg502Trp, has also been reported to be associated with HCM, suggesting that the Arg502 residue is likely important for MYBPC3 protein function. Fourteen submitters have provided assessments for this variant to ClinVar after 2014 and all classified the variant as pathogenic (n=13) or likely pathogenic (n=1). Based on the evidence outlined above, the variant was classified as pathogenic.

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 cardiomyopathy. (I) 0108 - This gene is known to be associated with both recessive and dominant disease. Heterozygous variants are frequently reported in adult onset hypertrophic and dilated cardiomyopathies, however recessive inheritance is associated with a severe early onset hypertrophic cardiomyopathy (OMIM). (I) 0115 - Variants in this gene are known to have variable expressivity (PMID: 32841044). (I) 0200 - Variant is predicted to result in a missense amino acid change from an arginine to glutamine. (I) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v3) <0.001 for a dominant condition (3 heterozygotes, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v3) (13 heterozygotes, 0 homozygotes). (I) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0600 - Variant is located in the annotated immunoglobulin I-set domain (NCBI). (I) 0801 - This variant has very strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported in multiple individuals with hypertrophic cardiomyopathy (ClinVar, PMID: 31308319, 31771441). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

This sequence change in MYBPC3 is predicted to replace arginine with glutamine at codon 502, p.(Arg502Gln). The arginine residue is highly conserved (100 vertebrates, Multiz Alignments), and is located in the Ig-like C2-type 3 domain in a region (amino acids 485-502), that is defined as a mutational hotspot (PMID: 30696458). There is a small physicochemical difference between arginine and glutamine. The highest population minor allele frequency in the population database gnomAD v4.1 is 0.007% (5/74,922 alleles) in the African/African American population. The prevalence of the variant in individuals with hypertrophic cardiomyopathy (HCM) is significantly increased compared with the prevalence in the population (30 in 11,582 case genotypes vs 5 in 589,947 control genotypes giving an odds ratio of 306.4, 95%CI=118.9-789.9; PMID: 20433692, 25611685, 28771489, 32481709, 37652022; gnomAD v4.1). The variant has been reported to segregate with HCM in multiple families (PMID: 9562578, 20433692). Computational evidence predicts a deleterious effect for the missense substitution (REVEL = 0.645). Another missense variant with a larger physicochemical difference (c.1504C>T p.Arg502Trp) in the same codon has been classified as pathogenic for HCM (ClinVar ID: 42540). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.6.1, this variant is classified as PATHOGENIC. Following criteria are met: PM1, PP1_Strong, PP3, PS4.

This heterozygous missense variant in the MYBPC3 gene was identified in a baby with neonatal hypertrophic cardiomyopathy.

This missense variant replaces arginine with glutamine at codon 502 in the Ig-like domain C3 of the MYBPC3 protein. Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. To our knowledge, functional studies have not been reported for this variant. This variant has been reported in over 20 individuals affected with hypertrophic cardiomyopathy (PMID: 9562578, 16566405, 18403758, 18533079, 20433692, 22112859, 22267749, 22857948, 27600940, 28193612, 31308319). It has been shown that this variant segregates with hypertrophic cardiomyopathy in multiple affected individuals across multiple unrelated families (PMID: 20433692, 22112859). This variant has also been reported in one individual affected with left ventricular noncompaction cardiomyopathy who also carried a different pathogenic truncation variant in the same gene (PMID: 31918855). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). A different variant affecting the same codon, p.Arg502Trp, is considered to be disease-causing (ClinVar variation ID: 42540), suggesting that arginine at this position is important for MYBPC3 protein function. Based on the available evidence, this variant is classified as Pathogenic.

Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.;Absent from controls (or at extremely low frequency if recessive) in Genome Aggregation Database, Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium.;Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc).;The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls.;Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 502 of the MYBPC3 protein (p.Arg502Gln). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with hypertrophic cardiomyopathy (PMID: 9562578, 16566405, 18403758, 18533079, 20433692, 22386539). ClinVar contains an entry for this variant (Variation ID: 42541). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. This variant disrupts the p.Arg502 amino acid residue in MYBPC3. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 12707239, 20378854, 22267749, 23396983). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

The variant is observed at an extremely low frequency in the gnomAD v4.1.0 dataset (total allele frequency: <0.001%). Predicted Consequence/Location: Missense variant In silico tool predictions suggest damaging effect of the variant on gene or gene product [REVEL: 0.65 (>=0.6, sensitivity 0.68 and specificity 0.92); 3Cnet: 0.79 (> 0.75, sensitivity 0.96 and precision 0.92)]. The same nucleotide change resulting in the same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000042541 /PMID: 9562578 /3billion dataset). The variant has been observed in multiple (>3) similarly affected unrelated individuals (PMID: 18533079, 9562578). Different missense changes at the same codon (p.Arg502Gly, p.Arg502Leu, p.Arg502Trp) have been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000042540, VCV000164112, VCV001475570 /PMID: 12707239, 26090888). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

The c.1505G>A (p.R502Q) alteration is located in exon 17 (coding exon 17) of the MYBPC3 gene. This alteration results from a G to A substitution at nucleotide position 1505, causing the arginine (R) at amino acid position 502 to be replaced by a glutamine (Q). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This variant has been reported in numerous individuals with hypertrophic cardiomyopathy (HCM) including several families with strong evidence of segregation with disease (Niimura, 1998; Cardim, 2005; Rudziski, 2008; Otsuka, 2012; Maurizi, 2018). This variant has also been reported in an individual with HCM who also had evidence of left ventricular noncompaction (Faria, 2012). This amino acid position is highly conserved in available vertebrate species. This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.

This missense variant replaces arginine with glutamine at codon 502 in the Ig-like domain C3 of the MYBPC3 protein. Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. To our knowledge, functional studies have not been reported for this variant. This variant has been reported in over 20 individuals affected with hypertrophic cardiomyopathy (PMID: 9562578, 16566405, 18403758, 18533079, 20433692, 22112859, 22267749, 22857948, 27600940, 28193612, 31308319). It has been shown that this variant segregates with hypertrophic cardiomyopathy in multiple affected individuals across multiple unrelated families (PMID: 20433692, 22112859). This variant has also been reported in one individual affected with left ventricular noncompaction cardiomyopathy who also carried a different pathogenic truncation variant in the same gene (PMID: 31918855). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). A different variant affecting the same codon, p.Arg502Trp, is considered to be disease-causing (ClinVar variation ID: 42540), suggesting that arginine at this position is important for MYBPC3 protein function. Based on the available evidence, this variant is classified as Pathogenic.

The MYBPC3 c.1505G>A variant is predicted to result in the amino acid substitution p.Arg502Gln. This variant has been reported to segregate with hypertrophic cardiomyopathy in multiple unrelated families (See for example – Niimura et al. 1998. PubMed ID: 9562578; Jordan et al. 2011. PubMed ID: 21310275; Table S1A/B in Walsh et al. 2017. PubMed ID: 27532257) and has been interpreted as pathogenic by multiple clinical labs in the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/variation/42541/). Additionally, different amino acid substitutions (p.Arg502Gly, p.Arg502Trp, p.Arg502Leu) affecting the same amino acid have been reported as pathogenic (Human Gene Mutation Database). We classify the c.1505G>A (p.Arg502Gln) variant as pathogenic.