A variant of uncertain significance has been identified in the MYBPC3 gene. The Y1251H variant has been reported as a rare variant in one individual from an HCM-affected cohort (Lopes et al. 2015); however, additional clinical information, segregation data and functional studies were not provided. Nevertheless, this variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The Y1251H variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. Finally, this substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function.

Variant classified as Uncertain Significance - Favor Pathogenic. The p.Tyr1251Hi s variant in MYBPC3 has not been previously reported in individuals with cardiom yopathy or in large population studies. Tyrosine (Tyr) at position 1251 is highl y conserved in mammals and across evolutionarily distant species and the change to Histidine (His) was predicted to be pathogenic using a computational tool cli nically validated by our laboratory. This tool's pathogenic prediction is estima ted to be correct 94% of the time (Jordan 2011). In summary, while there is some suspicion for a pathogenic role, the clinical significance of the p.Tyr1251His variant is uncertain.

The p.Y1251H variant (also known as c.3751T>C), located in coding exon 33 of the MYBPC3 gene, results from a T to C substitution at nucleotide position 3751. The tyrosine at codon 1251 is replaced by histidine, an amino acid with similar properties. This alteration has been reported in hypertrophic cardiomyopathy (HCM) cohorts; however, clinical details were limited (Lopes LR et al. Heart, 2015 Feb;101:294-301; Ingles J et al. Circ Cardiovasc Genet, 2017 Apr;10; Walsh R et al. Genet Med, 2017 02;19:192-203). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as 3A-VUS. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene. (N) 0108 - This gene is known to be associated with both recessive and dominant disease. Dominant inheritance is frequently reported in adult onset conditions, however recessive inheritance results in a more severe early onset phenotype (OMIM). (N) 0200 - Variant is predicted to result in a missense amino acid change from tyrosine to histidine (exon 33). (N) 0251 - Variant is heterozygous. (N) 0301 - Variant is absent from gnomAD. (P) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools, it is highly conserved with a moderate amino acid change. (P) 0600 - Variant is located in an annotated domain or motif (Immunoglobulin I-set domain; NCBI) (N) 0708 - Comparable variants have conflicting previous evidence for pathogenicity. p.(Tyr1251Cys) reported once in a cohort of 874 HCM patients and as a variant of uncertain significance in ClinVar (ClinVar; PMID: 25351510) (N) 0804 - Variant is absent in the population and has previously been described as variant of uncertain significance in multiple independent cases with consistent phenotype (ClinVar, PMID: 25351510, 28408708, 27532257) (P) 0905 - No segregation evidence has been identified for this variant. (N) 1007 - No published functional evidence has been identified for this variant. (N) 1208 - Inheritance information for this variant is not currently available. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign

This sequence change replaces tyrosine, which is neutral and polar, with histidine, which is basic and polar, at codon 1251 of the MYBPC3 protein (p.Tyr1251His). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with hypertrophic cardiomyopathy (PMID: 25351510, 33782553, 36578016, 37652022; internal data). ClinVar contains an entry for this variant (Variation ID: 181020). 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. Studies have shown that this missense change alters MYBPC3 gene expression (PMID: 34097875). For these reasons, this variant has been classified as Pathogenic.