MYBPC3 p.Pro679=
c.2037C>A · rs749317445 · VCV1150999
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.49e-05%, nfe)
Conditions
1
hypertrophic cardiomyopathy
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.39 | GERP -3.5, phastCons 0.98 |
| Overall | ||
| CADD | 5.558 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.49e-05%
European (non-Finnish) · 1/1,178,400 alleles
Overall
6.21e-05%
1/1,611,338 alleles · very rare
exomes 1/1,459,008 · genomes 0/152,330 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- MYBPC3
- Protein
- p.Pro679=
- Coding
- c.2037C>A
- MANE Select
- NM_000256
- dbSNP
- rs749317445
- Type
- single nucleotide variant
- Location
- chr11:47339681 (GRCh38)
- Gene constraint
- LOEUF 0.915 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 79.43 · 17 PDB
- Residue 679
- the ig-like c2-type 5 domain
Similar variants
- MYBPC3 p.Pro679Ser Uncertain significance ★★ ⚠ same residue
- MYBPC3 p.Pro679Thr Uncertain significance ★★ ⚠ same residue
- MYBPC3 p.Arg495Gln Likely pathogenic ★★★ ⚠ same condition
- MYBPC3 p.Arg495Gly Likely pathogenic ★★★ ⚠ same condition
- MYBPC3 p.Arg495Trp Likely pathogenic ★★★ ⚠ same condition
- MYBPC3 p.Arg502Gln Pathogenic ★★★ ⚠ same condition
- MYBPC3 c.26-2A>G Uncertain significance ★★★ same condition
- MYBPC3 p.Arg1271Ter Uncertain significance ★★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/mybpc3-p-pro679 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown