MYL2 p.Lys89=
c.267A>G · VCV3651773
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
Conditions
1
hypertrophic cardiomyopathy 10
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 -0.71 | GERP -5.7, phastCons 0.029 |
| Overall | ||
| CADD | 7.355 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,178,888 alleles
Overall
6.2e-05%
1/1,612,628 alleles · very rare
exomes 1/1,460,736 · genomes 0/151,892 · 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
- MYL2
- Protein
- p.Lys89=
- Coding
- c.267A>G
- MANE Select
- NM_000432
- Type
- single nucleotide variant
- Location
- chr12:110914193 (GRCh38)
- Gene constraint
- LOEUF 1.157 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 84.10 · 6 PDB
Similar variants
- MYL2 p.Gly162Glu Likely pathogenic ★★★ ⚠ same condition
- MYL2 p.Gln126Glu Uncertain significance ★★★ ⚠ same condition
- MYL2 p.Gly162Arg Uncertain significance ★★★ ⚠ same condition
- MYL2 p.Gly57Glu Uncertain significance ★★★ ⚠ same condition
- MYL2 p.Pro143Leu Uncertain significance ★★★ ⚠ same condition
- MYL2 p.Arg58Gln Pathogenic/Likely pathogenic ★★ same condition
- MYL2 p.Arg58Leu Likely pathogenic ★★ same condition
- MYL2 p.Asp166Val Pathogenic/Likely pathogenic ★★ 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/myl2-p-lys89 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown