MYO7A p.Lys269del
c.799AAG[2] · rs781896482 · VCV2137201
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000339%, nfe)
Conditions
1
Usher syndrome type 1B
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.3 | GERP -3.5, phastCons 0.98 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000339%
European (non-Finnish) · 4/1,179,274 alleles
Filtering AF
7.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.000248%
4/1,612,396 alleles · very rare
exomes 4/1,460,110 · genomes 0/152,286 · 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
- MYO7A
- Protein
- p.Lys269del
- Coding
- c.799AAG[2]
- MANE Select
- NM_000260
- dbSNP
- rs781896482
- Type
- Microsatellite
- Location
- chr11:77157340 (GRCh38)
- Gene constraint
- LOEUF 0.995 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.73 · 1 PDB
- Residue 269
- the myosin motor domain; a UniProt-annotated variant site (in ush1b)
Similar variants
- MYO7A p.Glu1716del Pathogenic/Likely pathogenic ★★ same condition
- MYO7A p.Phe1963del Pathogenic/Likely pathogenic ★★ same condition
- MYO7A p.Ser423fs Likely pathogenic ★★ same condition
- MYO7A p.Val1501fs Pathogenic/Likely pathogenic ★★ same condition
- MYO7A c.3924+31_3924+46del Benign/Likely benign ★★ same condition
- MYO7A p.Ala601fs Likely pathogenic ★ same condition
- MYO7A p.Lys269fs Pathogenic ★ same residue
- MYO7A p.Thr54fs 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/myo7a-p-lys269del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown