The MYBPC3 c.3763G>A; p.Ala1255Thr variant (rs727503167) is reported in the literature in numerous individuals affected with hypertrophic cardiomyopathy, including one individual with a pathogenic variant in trans in the same gene (Coppini 2014, Field 2022, Lopes 2013, Mademont-Soler 2017, Richard 2003). This variant has also been seen in one individual with dilated cardiomyopathy with a truncating variant in a different gene (Janin 2017). This variant is found in the general population with an overall allele frequency of 0.007% (19/280,328 alleles) in the Genome Aggregation Database (v2.1.1). An in vitro minigene assay demonstrates this variant does not affect splicing (Ito 2017). However computational analyses predict that this variant is deleterious (REVEL: 0.84). Due to conflicting information, the clinical significance of this variant is uncertain at this time. References: Coppini R et al. Clinical phenotype and outcome of hypertrophic cardiomyopathy associated with thin-filament gene mutations. J Am Coll Cardiol. 2014 Dec 23;64(24):2589-2600. PMID: 25524337. Field E et al. Cardiac myosin binding protein-C variants in paediatric-onset hypertrophic cardiomyopathy: natural history and clinical outcomes. J Med Genet. 2022 Aug;59(8):768-775. PMID: 34400558. Ito K et al. Identification of pathogenic gene mutations in LMNA and MYBPC3 that alter RNA splicing. Proc Natl Acad Sci U S A. 2017 Jul 18;114(29):7689-7694. PMID: 28679633. Janin A et al. Truncating mutations on myofibrillar myopathies causing genes as prevalent molecular explanations on patients with dilated cardiomyopathy. Clin Genet. 2017 Dec;92(6):616-623. PMID: 28436997. Lopes LR et al. Genetic complexity in hypertrophic cardiomyopathy revealed by high-throughput sequencing. J Med Genet. 2013 Apr;50(4):228-39. PMID: 23396983. Mademont-Soler I et al. Additional value of screening for minor genes and copy number variants in hypertrophic cardiomyopathy. PLoS One. 2017 Aug 3;12(8):e0181465. PMID: 28771489. Richard P et al. Hypertrophic cardiomyopathy: distribution of disease genes, spectrum of mutations, and implications for a molecular diagnosis strategy. Circulation. 2003 May 6;107(17):2227-32. PMID: 12707239.

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

This missense variant replaces alanine with threonine at codon 1255 of the MYBPC3 protein. Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. A minigene assay suggests that this variant does not affect normal RNA splicing (PMID: 28679633), however the clinical relevance of this observation is unknown. This variant has been reported in individuals affected with hypertrophic cardiomyopathy (PMID: 12707239, 20031618, 23396983, 25524337, 25351510, 27532257, 28771489, 33782553). It has also been reported in two individuals affected with peripartum cardiomyopathy (PMID: 33874732), in two individuals affected with an unspecified cardiomyopathy (PMID: 37477868), in one individual affected with dilated cardiomyopathy (PMID: 28436997), and in one individual affected with sudden cardiac arrest (PMID: 37194601). This variant has been identified in 19/280328 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

Identified in a 31-year-old female with familial dilated cardiomyopathy (DCM); however, this individual also harbored a truncating FLNC variant (PMID: 28436997); 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: 25524337, 28840316, 24793961, 27532257, 12707239, 23396983, 15115610, 28679633, 28771489, 25351510, 20031618, 28518168, Komissarova2021[article], Komissarova2022[article], 34400558, 33782553, 37652022, 28436997)

Variant summary: MYBPC3 c.3763G>A (p.Ala1255Thr) results in a non-conservative amino acid change located in the Immunoglobulin I-set domain (IPR013098) of the encoded protein sequence. Four of four in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 6.8e-05 in 248930 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in MYBPC3 causing Hypertrophic Cardiomyopathy (6.8e-05 vs 0.001), allowing no conclusion about variant significance. c.3763G>A has been reported in the heterozygous state in the literature in numerous individuals affected with Hypertrophic Cardiomyopathy or, rarely, other cardiac conditions (example, Bos_2014, Chumakova_2023, Coppini_2014, Goli_2021, Lopes_2015, Janin_2017, Kaski_2009, Lopes_2013, Mademont-Soler_2017, Mazzarotto_2018, McGurk_2023, Richard_2003, Thompson_2021, Walsh_2017). Further, it has also been reported in the biallelic state with two distinct likely pathogenic/pathogenic variants in at least 2 individuals with pediatric onset Hypertrophic Cardiomyopathy (Field_2022), however to our knowledge there is not currently a well-established recessive gene-disease association for MYBPC3. These report(s) do not provide unequivocal conclusions about association of the variant with Hypertrophic Cardiomyopathy. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported, though an in vitro splicing study suggested no impact to splicing (Ito_2017). The following publications have been ascertained in the context of this evaluation (PMID: 24793961, 38002985, 25524337, 34400558, 33874732, 28679633, 28436997, 20031618, 23396983, 28771489, 29875424, 37652022, 12707239, 33782553, 27532257, 25351510). ClinVar contains an entry for this variant (Variation ID: 164023). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.

This sequence change in MYBPC3 is predicted to replace alanine with threonine at codon 1255, p.(Ala1255Thr). The alanine residue is highly conserved (100 vertebrates, Multiz Alignments), and is located in the IG-like C2 Type domain 7 in a region (amino acids 1248-1266) defined as a mutational hotspot for hypertrophic cardiomyopathy (HCM, PMID: 30696458). There is a small physicochemical difference between alanine and threonine. The highest population minor allele frequency in the population database gnomAD v4.1 is 0.01% (13/60,012 alleles) in the Admixed American population. This variant has been reported in multiple individuals with HCM and at least one individual with dilated cardiomyopathy (PMID: 27532257, 38836037, 28436997). Computational evidence predicts a deleterious effect for the missense substitution (REVEL = 0.840). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.7.0, this variant is classified as a VARIANT OF UNCERTAIN SIGNIFICANCE. Following criteria are met: PM1, PP3.

The p.Ala1255Thr variant in MYBPC3 has been identified in 7 individuals with hypertrophic cardiomyopathy, including one individual who also carried a heterozygous, likely pathogenic variant in another gene (Richard 2003, Lopes 2013, Coppini 2014, Walsh 2017, LMM data). It was also reported in 1 individual with DCM who also carried a frameshift variant in FLNC (Janin 2017). It has been identified in 0.028% (10/35350) of Latino chromosomes by gnomAD (http://gnomad.broadinstitute.org) and reported in ClinVar (Variation ID# 164023). Computational prediction tools and conservation analysis suggest that the p.Ala1255Thr variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: BS1_Supporting, PP3.

This missense variant replaces alanine with threonine at codon 1255 of the MYBPC3 protein. Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. A minigene assay suggests that this variant does not affect normal RNA splicing (PMID: 28679633), however the clinical relevance of this observation is unknown. This variant has been reported in individuals affected with hypertrophic cardiomyopathy (PMID: 12707239, 20031618, 23396983, 25524337, 25351510, 27532257, 28771489, 33782553). It has also been reported in two individuals affected with peripartum cardiomyopathy (PMID: 33874732), in two individuals affected with an unspecified cardiomyopathy (PMID: 37477868), in one individual affected with dilated cardiomyopathy (PMID: 28436997), and in one individual affected with sudden cardiac arrest (PMID: 37194601). This variant has been identified in 19/280328 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 1255 of the MYBPC3 protein (p.Ala1255Thr). This variant is present in population databases (rs727503167, gnomAD 0.03%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with hypertrophic cardiomyopathy (PMID: 12707239, 20031618, 23396983, 25351510, 25524337, 27532257, 33782553, 34400558, 38002985). ClinVar contains an entry for this variant (Variation ID: 164023). 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 available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.