NM_000256.3(MYBPC3):c.2573G>A (p.Ser858Asn). This variant has been in individuals with HCM (ClinVar Variation ID: 164070) and has also been identified in 2 out of 124800 (0.005% FAF 95% CI) of European chromosomes in gnomAD (https://gnomad.broadinstitute.org/; v.2.1). This variant is statistically increased in individuals with HCM compared to controls (OR lower 95% CI>5), therefore, the PS4 criterion has been applied at supporting strength (PS4_Supporting) and the PM2_Supporting criterion has not been applied. Computational prediction tools and conservation analyses suggest that this variant may impact the protein (PP3; REVEL score ≥0.70). In summary, due to insufficient evidence, this variant is classified as uncertain significance for hypertrophic cardiomyopathy in an autosomal dominant manner based on PS4_Supporting, and PP3.

The p.S858N variant (also known as c.2573G>A), located in coding exon 25 of the MYBPC3 gene, results from a G to A substitution at nucleotide position 2573. The serine at codon 858 is replaced by asparagine, an amino acid with highly similar properties. This alteration has been reported in patients with hypertrophic cardiomyopathy (HCM) and HCM genetic testing cohorts; however, other variants in cardiomyopathy-associated genes were detected in some cases and/or clinical detail was limited (Morita H et al. N. Engl. J. Med. 2008;358:1899-908; Walsh R et al. Genet. Med. 2017;19:192-203; Norrish G et al. Circulation. 2019 Jul;140(3):184-192; Field E et al. J Med Genet. 2022 Aug;59(8):768-775). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Based on the available evidence, the clinical significance of this variant remains unclear.

This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 858 of the MYBPC3 protein (p.Ser858Asn). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with hypertrophic cardiomyopathy (PMID: 20378854, 27532257, 31006259). ClinVar contains an entry for this variant (Variation ID: 164070). 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.

The c.2573G>A p.Ser858Asn variant (rs727503185) has been reported in at least 6 individuals with hypertrophic cardiomyopathy (Morita. 2008, and Walsh 2017). However, in at least one individual the p.Ser858Asn variant was identified with another pathogenic variant of MYBPC3 and family segregation data of the p.Ser858Asn variant was not readily available for any of the individuals. This variant is reported as a variant of uncertain significance by 5 laboratories in ClinVar (Variation ID: 164070). This variant is only observed on two alleles in the Genome Aggregation Database, indicating it is not a common polymorphism. The serine at codon 858 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Due to limited information, the clinical significance of the p.Ser858Asn variant is uncertain at this time.

Reported in association with cardiomyopathy; however, at least one family harbored an additional pathogenic variant in the MYBPC3 gene (Morita et al., 2008; Saltzman et al., 2010; Ho et al., 2013; Walsh et al., 2017); 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: 23549607, 20378854, 18403758, 18761664, 27532257, 25228707, 31006259)

The p.Ser858Asn variant in MYPBC3 has been identified in at least 12 individuals with HCM and segregated with disease in 1 affected family member (Walsh 2017 PMID: 27532257, Ambry pers. comm., GeneDx pers. comm., Invitae pers. comm., LMM data). Additionally, it was identified in several individuals, some with earlier onset or more severe presentations, who carried additional pathogenic variants in other cardiomyopathy related genes (Ambry pers. Comm., Invitae pers. Comm., GeneDx pers. comm.). This variant has also been reported in ClinVar (Variation ID # 164070) and has been identified in 2/124800 of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). Computational prediction tools and conservation analysis suggest that this 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, PM2_Supporting, PP3.

The p.Ser858Asn variant in the MYBPC3 gene has been previously reported in the heterozygous in at least 6 unrelated individuals with HCM and in the compound heterozygous state with another pathogenic variant (p.Arg502Trp) in an individual with childhood-onset HCM (PMID: 27532257; PMID: 18403758). This variant has also been identified in 2/124,800 European (non-Finnish) chromosomes by the Genome Aggregation Database (http://gnomad.broadinstitute.org/). This variant is present in ClinVar (Accession: VCV000164070.37). This variant is located in the C6 domain of MYBPC3. Other pathogenic and likely pathogenic variants have been described in this domain and disrupt the function of MYBPC3 (PMID: 32841044). Computational tools predict that this variant is deleterious; however, the accuracy of in silico algorithms is limited. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, there is sufficient evidence to classify the p.Ser858Asn variant as likely pathogenic for autosomal dominant HCM based on the information above. [ACMG evidence codes used: PS4_moderate; PM2; PM1_supporting; PP3]

MYBPC3: PM2, PM5, PS4:Moderate