The MYBPC3 c.1591G>A (p.Gly531Arg) missense variant has been reported in two individuals with hypertrophic cardiomyopathy (HCM) and one with dilated cardiomyopathy (PMID: 21750094; 33673806). A c.1591G>C variant, which results in the same amino acid change, has been reported in at least five unrelated individuals with HCM and has been shown to segregate with the disease in the affected child of one proband (PMID: 21835320; 24793961; 25351510; 27532257; doi:10.1016/j.genrep.2021.101471). The c.1591G>C variant has also been reported in two individuals with early-onset disease who carried a second variant in MYBPC3 (PMID: 27483260). In addition, the p.Gly531Arg variant has been identified in at least three additional individuals with HCM without the nucleotide change being specified (PMID: 16858239; 20031602; 22765922). The c.1591G>A variant is not observed at a significant frequency in version 2.1.1 or version 3.1.2 of the Genome Aggregation Database. Multiple lines of computational evidence suggest the variant may have a deleterious effect on the gene or gene product. Functional studies demonstrated that the c.1591G>A (p.Gly531Arg) variant was unable to restore maximal force to the wild-type level when it was co-expressed with the wild-type protein in engineered heart tissue from MYBPC3 knock-out mice (PMID: 27108529). Based on the available evidence, the c.1591G>A (p.Gly531Arg) variant is classified as likely pathogenic for hypertrophic cardiomyopathy.

The c.1591G>A (p.Gly531Arg) variant of the MYBPC3 gene replaces glycine with arginine at codon 531 of the MYBPC3 protein. This variant has been reported in more than 10 unrelated individuals affected with hypertrophic cardiomyopathy (HCM) (PMID: 18533079, 20624503, 21750094, 23508784, 27483260, 27532257, 27600940, 28356264, 33673806, 21835320,33673806). A functional study in which the c.1591G>C (p.Gly531Arg) variant was transfected into MYBPC3 knockout mouse cardiomyocytes alone and in combination with wild-type MYBPC3 (to represent homozygous and heterozygous disease states) revealed abnormal contractile force in both scenarios compared to wild-type (PMID: 27108529). In addition, an alternative nucleotide change resulting in the same protein change (c.1591G>C; p.Gly531Arg) has been classified as likely pathogenic for autosomal dominant HCM by 7 submitters in ClinVar (Variation ID: 42550). Computational evidence supports a deleterious effect on the protein structure and function (REVEL score 0.854). This variant has been identified in 8/247086 chromosomes in the general population (gnomAD). Based on these evidence, the c.1591G>A (p.Gly531Arg) variant of the MYBPC3 gene is interpreted as likely pathogenic.

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Likely pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with hypertrophic cardiomyopathy 4 (HCM; MIM#115197). (I) 0108 - This gene is associated with both recessive and dominant disease. Dominant inheritance is frequently reported in adult-onset conditions and recessive inheritance results in a more severe early onset phenotype (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 glycine to arginine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2 and v3 (non-v2)) <0.01 (12 heterozygotes, 0 homozygotes). A different nucleotide substitution resulting in the same amino acid change has also been observed in gnomAD (v2 and v3 (non-v2): 8 heterozygotes, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v3) (p.(Gly531Trp): 1 heterozygote, 0 homozygotes). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated Immunoglobulin I-set domain (DECIPHER). (I) 0710 - Another missense variant comparable to the one identified in this case has inconclusive previous evidence for pathogenicity. The p.(Gly531Trp) variant has been classified as a VUS by multiple clinical diagnostic laboratories (ClinVar). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant (G>A) and a different nucleotide substitution (G>C), which result in the same amino acid change, have been classified as likely pathogenic and pathogenic by multiple clinical diagnostic laboratories and have been reported in multiple individuals with HCM (ClinVar; Atlas of Cardiac Genetic Variation; PMIDs: 21750094, 24793961, 28356264, 31941943, 32841044, 36291626). Additionally, this amino acid change has also been classified as a VUS by two clinical diagnostic laboratories and has also been reported in one individual with left ventricular noncompaction cardiomyopathy (ClinVar; PMID: 28798025). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Mutant constructs (c.1591G>C; p.(Gly531Arg)) transfected into knockout engineered heart cells mice tissues and expressed either as heterozygous or homozygous demonstrated abnormal force and contraction velocity compared to WT (PMID: 27108529). (SP) 1205 - This variant has been shown to be maternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

This missense variant replaces glycine with arginine at codon 531 of the MYBPC3 protein (c.1591G>A; p.Gly531Arg). Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). A functional study has shown that a different nucleotide change with the same protein effect (c.1591G>C; p.Gly531Arg) does not fully rescue the hypercontractile phenotype of heart tissue from Mybpc3 knockout mouse (PMID: 27108529). Considering both c.1591G>A and c.1591G>C nucleotide changes, the p.Gly531Arg missense variant has been reported in over 10 individuals affected with hypertrophic cardiomyopathy (PMID: 16858239, 18533079, 19150014, 20624503, 21750094, 21835320, 22765922, 23508784, 27483260, 27532257, 28356264, 32369506, 33495597, 33673806). Two of these individuals carried a different pathogenic variant in the same gene (PMID: 20624503, 27483260), and one of them showed early-onset of disease before age 25 (PMID: 27483260). This variant has been identified in 8/247086 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic.

The p.G531R variant (also known as c.1591G>A), located in coding exon 17 of the MYBPC3 gene, results from a G to A substitution at nucleotide position 1591. The glycine at codon 531 is replaced by arginine, an amino acid with dissimilar properties. This variant and another variant leading to the same amino acid substitution (MYBPC3 c.1591G>C) have been reported in multiple unrelated patients with hypertrophic cardiomyopathy (HCM) (Girolami F et al. J Cardiovasc Med (Hagerstown), 2006 Aug;7:601-7; Olivotto I et al. Mayo Clin Proc, 2008 Jun;83:630-8; Garc&iacute;a-Castro M et al. Rev Esp Cardiol, 2009 Jan;62:48-56; Ho CY et al. Circ Cardiovasc Genet, 2009 Aug;2:314-21; Millat G et al. Eur J Med Genet, 2010 Jul;53:261-7; Waldm&uuml;ller S et al. Eur J Heart Fail, 2011 Nov;13:1185-92; Lopes LR et al. Heart, 2015 Feb;101:294-301; Rubattu S et al. Int J Mol Sci, 2016 Jul;17:[ePub ahead of print]; Walsh R et al. Genet Med, 2017 Feb;19:192-203; external communication; Ambry internal data). In a functional study utilizing engineered heart tissue derived from MYBPC3 knockout cardiomyocytes, c.1591G>C p.G531R was unable to completely rescue the hypercontractile phenotype of the knockout tissue; however, the physiological relevance of this result is unclear (Wijnker PJ et al. J. Mol. Cell. Cardiol. 2016;97:82-92). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic.

PS1, PS4, PS3_mod, PM2

Absent from controls (or at extremely low frequency if recessive) in Genome Aggregation Database, Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium.;The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls.;Patient's phenotype or family history is highly specific for a disease with a single genetic etiology.;Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc).

Published functional studies suggest a damaging effect in mouse engineered heart tissue (PMID: 27108529); 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: 16858239, 27532257, 20031602, 19150014, 20173211, 20594303, 21750094, 22765922, 23690394, 23508784, 27590665, 28356264, 28193612, 28152038, 28679633, 33673806, 39260623, 32369506, 38259611, 35130036, Emrahi2022, 36264615, 37652022, 18533079, 39669589, 38374194, 38456273, 27108529, 39486665, 34714385)

Variant summary: MYBPC3 c.1591G>A (p.Gly531Arg) results in a non-conservative amino acid change in the encoded protein sequence. Algorithms developed to predict the effect of missense changes on protein structure and function all suggest that this variant is likely to be disruptive. The variant allele was found at a frequency of 3.2e-05 in 247486 control chromosomes. c.1591G>A has been observed in individual(s) affected with Cardiomyopathy (Coto_2012, Coto_2010, DiDonna_2010, Garcia-Castro_2009, Girolami_2006, Ho_2013, Waldmuller_2011, Olivotto_2008, Valente_2013, Sequeira_2013, Hathaway_2021). These data indicate that the variant is likely to be associated with disease. A different variant resulting in the same amino acid consequence has been classified as likely pathogenic by our lab (c.1591G>C, p.Gly531Arg), supporting the pathogenicity of this variant. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 22765922, 20594303, 20173211, 19150014, 16858239, 33673806, 23549607, 18533079, 23508784, 23690394, 21750094). ClinVar contains an entry for this variant (Variation ID: 164109). Based on the evidence outlined above, the variant was classified as likely pathogenic.

This is a nonsynonymous variant in the MYBPC3 gene (OMIM: 600958). Pathogenic variants in this gene have been associated with autosomal dominant hypertrophic cardiomyopathy 4. This variant has been reported in the heterozygous state in at least many unrelated affected individuals (PMID: 33673806, 28798025, 27532257, 27600940, 27483260, 25351510). Multiple computational algorithms predict a deleterious effect for this variant (REVEL score: 0.854) (PP3) and an alternate nucleotide substitution resulting in the same amino acid change (c.1591G>C) has been previously reported as pathogenic (PMID: 27108529) (PS1). This variant has a 0.0089% maximum allele frequency in non-founder control populations (https://gnomad.broadinstitute.org/). Based on the current evidence, this variant is classified as likely pathogenic for autosomal dominant hypertrophic cardiomyopathy 4.

MYBPC3: PS1, PS4:Moderate, PM2:Supporting, PS3:Supporting

PP3, PM2, PS3_supporting, PS4_moderate

The p.Gly531Arg variant in MYBPC3 has been reported in association with two distinct nucleotide changes: c.1591G>C and c.1591G>A. Considering both nucleotide changes, this variant has been reported in 1 individual with dilated cardiomyopathy (DCM; c.1591G>A; Waldmuller 2011 PMID: 21750094) and in over 10 individuals with hypertrophic cardiomyopathy (HCM; c.1591G>A: Girolami 2006 PMID: 16858239, Olivotto 2008 PMID: 18533079, Garcia-Castro 2009 PMID: 19150014, Michels 2011, Waldmuller 2011 PMID: 21750094, Walsh 2017 PMID: 27532257, LMM data; c.1591G>C: Millat 2010 PMID: 20624503, Olivotto 2011 PMID: 21835320, Coto 2012 PMID: 22765922, Rubattu 2016 PMID: 27483260, LMM data). Of the individuals with HCM, at least 4 individuals carried a second pathogenic MYBPC3 variant and had early onset disease (LMM data, Millat 2010 PMID: 20624503, Rubattu 2016 PMID: 27483260). Furthermore, the c.1591G>C variant was found by our laboratory to segregate with disease in 2 affected relatives from 1 family. This variant has also been reported by other clinical laboratories in ClinVar (Variation IDs: 164109 (c.1591G>A) and 42550 (c.1591G>C)). Additionally, the c.1591G>A variant has been identified in 0.005% (1/17952) of East Asian and in 0.005% (6/111606) of European chromosomes by gnomAD, while the c.1591G>C variant has been identified in 0.003% (4/127020) of European chromosomes and 0.004% (1/24164) of African chromosomes in gnomAD (https://gnomad.broadinstitute.org/). A functional study in which the c.1591G>C (p.Gly531Arg) variant was transfected into MYBPC3 knockout mouse cardiomyocytes alone and in combination with wild-type MYBPC3 (to represent homozygous and heterozygous disease states) revealed abnormal contractile force in both scenarios compared to wild-type (Wijnker 2016 PMID: 27108529). Computational prediction tools and conservation analysis also suggest that the variant may impact the protein. In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal dominant HCM. ACMG/AMP Criteria applied: PS4_Moderate, PM2_Supporting, PS3_Moderate, PP3.

ACMG criteria used: PS1, PS4_Moderate

This missense variant replaces glycine with arginine at codon 531 of the MYBPC3 protein (c.1591G>Ap.Gly531Arg). Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. A functional study has shown that a different nucleotide change with the same protein effect (c.1591G>Cp.Gly531ArgClinVar variation ID: 164109) was unable to rescue the hypercontractile phenotype of heart tissue from Mybpc3 knockout mouse (PMID: 27108529). Considering both c.1591G>A and c.1591G>C nucleotide changes, the p.Gly531Arg missense variant has been reported in over 15 individuals affected with hypertrophic cardiomyopathy (PMID: 16858239, 18533079, 19150014, 20624503, 21750094, 21835320, 22765922, 23508784, 27483260, 27532257, 28356264, 32369506, 33495597, 33673806, 33782553, 36291626, 38259611, 38938358). Two of these individuals also carried a different pathogenic variant in the same gene (PMID: 20624503, 27483260), and one of them showed early-onset of disease before age 25 (PMID: 27483260). This variant has been identified in 8/247086 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic.

This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 531 of the MYBPC3 protein (p.Gly531Arg). This variant is present in population databases (rs397515912, gnomAD 0.006%). This missense change has been observed in individuals with hypertrophic cardiomyopathy (PMID: 18533079, 20624503, 21750094, 23508784, 27483260, 27532257, 27600940, 28356264, 31941943, 33673806, 36291626). ClinVar contains an entry for this variant (Variation ID: 164109). 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. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.