rs397515953 — MYBPC3

Rare pathogenic/likely pathogenic missense variant in the C5 immunoglobulin-like domain of cardiac myosin-binding protein C, disrupting sarcomere assembly and causing hypertrophic cardiomyopathy through haploinsufficiency (autosomal dominant)

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MYBPC3 C5 Domain — When a Structural Hinge in the Heart Breaks

Every heartbeat depends on a choreography of proteins that contract precisely and relax completely. At the heart of this machinery sits cardiac myosin-binding protein C (cMyBP-C)11 cardiac myosin-binding protein C (cMyBP-C)
encoded by MYBPC3, this 1,274 amino acid protein acts as both a structural scaffold of the cardiac thick filament and a regulatory brake on myosin-actin interaction; it is phosphorylated by PKA during exercise to allow the heart to increase output, which integrates the myosin motor machinery into a regulated, ordered structure called the sarcomere. Pathogenic variants in MYBPC3 are the single most common identified genetic cause of hypertrophic cardiomyopathy (HCM)22 hypertrophic cardiomyopathy (HCM)
abnormal thickening of heart muscle, particularly the interventricular septum, impairing ventricular filling and increasing the risk of dangerous arrhythmias, accounting for 40–50% of all genetically solved HCM cases globally.

This variant falls within the C5 immunoglobulin-like domain of cMyBP-C — one of ten immunoglobulin (Ig-like) and fibronectin type-III repeat units that form the protein's modular scaffold. The C5 domain is structurally unusual: it carries a 28-amino acid cardiac-specific insertion loop33 28-amino acid cardiac-specific insertion loop
absent from the skeletal muscle paralogs, sMyBP-C and fMyBP-C; the cardiac-specific loop has been proposed to mediate unique interactions with titin and other thick-filament components during sarcomere assembly present only in the cardiac isoform. This loop and the surrounding C5 Ig fold mediate key protein-protein interactions — particularly with titin — that anchor cMyBP-C in the correct sarcomeric register. Missense variants in C5 that disrupt these interfaces impair sarcomere assembly and reduce functional cMyBP-C protein, triggering HCM.

The Mechanism

Unlike the majority of MYBPC3 pathogenic variants (approximately 91% of which are truncating frameshift, splice, or nonsense mutations), missense variants like this one in C5 produce full-length protein with a single amino acid substitution. However, functional studies of MYBPC3 missense variants demonstrate that the disease mechanism converges on the same endpoint: haploinsufficiency44 haploinsufficiency
reduction of functional cMyBP-C protein to approximately half its normal level, which is insufficient to maintain proper sarcomere architecture and cross-bridge regulation.

Human myectomy data from confirmed MYBPC3 pathogenic variant carriers55 Human myectomy data from confirmed MYBPC3 pathogenic variant carriers
Marston et al. 2009, Circulation Research — examined 37 myectomy samples including both truncating and missense MYBPC3 mutations demonstrated that full-length MyBP-C protein was reduced approximately 24% versus donor controls (p<0.0005), with no truncated peptides detected. This rules out a dominant-negative poison protein mechanism: the mutant protein is either unstable and degraded, or fails to incorporate into sarcomeres, leaving the sarcomere with half its normal cMyBP-C complement.

The consequence of reduced cMyBP-C is dysregulated myosin cross-bridge kinetics: unrestrained myosin motors fire more frequently and asynchronously during both systole and diastole. The heart compensates through concentric hypertrophy — thickening its walls — which initially maintains output but progressively stiffens the ventricle, impairs diastolic filling, and creates a substrate for dangerous arrhythmias.

The Evidence

Helms et al. 202066 Helms et al. 2020
Spatial and Functional Distribution of MYBPC3 Pathogenic Variants and Clinical Outcomes; n=1,316 MYBPC3 HCM patients from the Sarcomeric Human Cardiomyopathy Registry established that nontruncating (missense) MYBPC3 pathogenic variants cluster significantly in the C3, C6, and C10 domains (82% of missense variants, p<0.001), with C5 being adjacent to these hotspot regions. Clinical outcomes for missense variant carriers were comparable to truncating variant carriers — both groups experienced similar rates of the composite adverse outcome (sudden cardiac death, resuscitated arrest, ICD therapy, transplant, LVAD, severe heart failure, atrial fibrillation, and stroke). This demonstrates that a single missense in a critical domain like C5 is as clinically consequential as a complete loss-of-function truncation.

MYBPC3 HCM follows incomplete, age-dependent penetrance77 incomplete, age-dependent penetrance
not all variant carriers develop detectable HCM during their lifetime; those who do often present late. A founder mutation cohort study found penetrance of approximately 39% in male carriers under 40, rising to 86% by age 60. Female carriers show lower early penetrance (~9% under 40) but nearly equivalent late penetrance (83% over 60). Genotype-positive, phenotype-negative carriers exhibit subtle ECG and biomarker differences from unaffected relatives even before left ventricular hypertrophy appears — underscoring the need for structured surveillance even in the apparently unaffected.

Aging further exacerbates the HCM phenotype88 Aging further exacerbates the HCM phenotype
three pathogenic pathways — nonsense- mediated mRNA decay, aberrant splicing, and ubiquitin-proteasome degradation of unstable mutant protein — all contribute to progressive haploinsufficiency, and aging hallmarks such as mitochondrial dysfunction and proteostatic stress amplify these effects over the lifetime of a carrier, explaining why the phenotype often worsens with age even without a new genetic event.

Practical Actions

Identifying a MYBPC3 C5 domain pathogenic carrier changes clinical management in ways that directly affect long-term outcomes. The 2024 AHA/ACC HCM guidelines recommend formal cardiac evaluation for all genotype-positive individuals and structured surveillance for those who are phenotype-negative at baseline. Mavacamten — a cardiac myosin inhibitor approved in 2022 — directly counteracts the sarcomeric hypercontractility caused by cMyBP-C haploinsufficiency and is now guideline-directed first-line therapy for symptomatic obstructive HCM (LVOT gradient ≥30 mmHg).

Each biological child, sibling, and parent of a MYBPC3 C5 domain variant carrier has a 50% chance of inheriting the pathogenic allele. Cascade genetic testing followed by structured cardiac surveillance in positive relatives enables early phenotypic detection and intervention before irreversible remodeling occurs.

Interactions

MYBPC3 missense variants in C5 operate through haploinsufficiency — a single pathogenic copy reduces total cMyBP-C protein enough to cause disease. Compound heterozygosity (two pathogenic MYBPC3 variants in trans, one on each chromosome) is rare but associated with severe, often neonatal-onset cardiomyopathy because the total functional protein falls to near-zero levels.

Co-inheritance with pathogenic variants in other sarcomere genes — particularly MYH7 (beta-myosin heavy chain), TNNT2 (cardiac troponin T), and TPM1 (alpha-tropomyosin, e.g. rs104894502) — constitutes "double-positive" HCM, associated with earlier onset and more severe hypertrophy than single-gene HCM. No published studies have specifically quantified the combined risk for MYBPC3 C5 domain missense plus variants in these other genes, but current clinical guidelines recommend treating double-positive genotypes as high-risk for risk stratification purposes.

Genotype Interpretations

What each possible genotype means for this variant.

CC Non-carrier Normal

No MYBPC3 C5 domain variant detected — no elevated risk from this locus

You carry two copies of the reference C allele at this position and do not carry the rare MYBPC3 C5 domain pathogenic variant. The vast majority of people (>99.99%) share this genotype. Your MYBPC3 gene is unaffected at this specific site, and you face no elevated risk of MYBPC3 C5 missense-related hypertrophic cardiomyopathy.

Note that HCM can be caused by pathogenic variants in many other genes — MYBPC3 alone has over 1,500 documented pathogenic alleles, and MYH7, TNNT2, TNNI3, TPM1, MYL2, MYL3, and ACTC1 also cause HCM. This result addresses only this specific MYBPC3 C5 domain variant and does not rule out other hereditary cardiomyopathy causes.

CT Pathogenic Carrier Carrier

MYBPC3 C5 domain pathogenic variant detected — hereditary HCM risk, specialist evaluation warranted

The MYBPC3 C5 domain (approximately residues 720–822 of the 1,274 aa cardiac isoform) folds into an immunoglobulin-like beta-sandwich structure stabilized by the hydrophobic core. It contains a 28-amino acid insertion loop present only in the cardiac isoform — absent from skeletal muscle paralogs — that mediates key contacts with titin and other thick-filament proteins during sarcomere assembly.

A missense substitution in C5 replaces a conserved residue at a position critical for domain stability or inter-domain contacts. The result is that the mutant cMyBP-C is either thermodynamically destabilized and degraded by the ubiquitin-proteasome system, or structurally altered such that it fails to incorporate into the sarcomeric A-band at its normal stoichiometry. Either way, total functional cMyBP-C protein drops to approximately 75–80% of normal — sufficient to impair cross-bridge regulation.

The deficit in cMyBP-C removes the molecular brake from the myosin motors: more cross-bridges are simultaneously active during both systole and diastole. The heart compensates with compensatory hypertrophy, thickening its walls to maintain stroke volume. Over time this creates diastolic stiffness (impaired ventricular relaxation), elevated filling pressures, and an arrhythmogenic substrate — interstitial fibrosis detectable on cardiac MRI as late gadolinium enhancement. The LGE burden correlates with sudden cardiac death risk.

Clinical manifestations in carriers can range from asymptomatic left ventricular hypertrophy found on a screening echocardiogram to exertional dyspnea, angina, near-syncope, or sudden cardiac death. The 2024 AHA/ACC HCM guidelines (PMID 38718139) recommend ECG and cardiac imaging every 3–5 years for phenotype-negative adult carriers, and annual monitoring for adolescent carriers (ages 10–20). Mavacamten, approved in 2022, is the first disease-specific therapy targeting the sarcomeric hypercontractility at the root of obstructive HCM.

This result must be confirmed by a CLIA-certified clinical laboratory before medical decisions are made. Consumer and research genotyping for ultra-rare pathogenic variants carries a meaningful false-positive rate.

TT Homozygous Homozygous

Carries two copies of MYBPC3 C5 domain pathogenic variant — severe HCM risk, extremely rare

You appear to carry two copies of the MYBPC3 C5 domain pathogenic missense variant, one on each chromosome 11. This is an extraordinarily rare genotype — the pathogenic T allele has a global frequency of approximately 1–3 per 100,000 at best, making biallelic inheritance exceedingly improbable. If this result is accurate, it implies both of your MYBPC3 copies are functionally compromised, which would reduce cMyBP-C protein to very low or near-absent levels.

Biallelic MYBPC3 pathogenic variants are documented in the literature as a cause of severe, neonatal-onset or infant-onset cardiomyopathy with rapid progression to heart failure. This is qualitatively different from the typical adult-onset penetrance seen in heterozygous MYBPC3 carriers. This result requires urgent verification at a CLIA-certified clinical laboratory and immediate specialist evaluation.