MYO7A p.Ala2039=
c.6117G>A · rs766671559 · VCV1099730
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00576%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -10 | GERP -3.2 |
| Overall | ||
| CADD | 4.065 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00576%
South Asian · 5/86,828 alleles
Filtering AF
0.00218%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00142%
Overall
0.00145%
23/1,591,490 alleles · very rare
exomes 19/1,439,312 · genomes 4/152,178 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00576% | 17,366 |
| East Asian | 0.00457% | 21,901 |
| African / African-American | 0.00268% | 37,273 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,656 |
| European (non-Finnish) | 0.00111% | 89,953 |
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.Ala2039=
- Coding
- c.6117G>A
- MANE Select
- NM_000260
- dbSNP
- rs766671559
- Type
- single nucleotide variant
- Location
- chr11:77211217 (GRCh38)
- Gene constraint
- LOEUF 0.995 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.73 · 1 PDB
- Residue 2039
- the ferm 2 domain; an α-helix
Similar variants
- MYO7A p.Ala2039Val Uncertain significance ★★ ⚠ same residue
- MYO7A p.Ala2039Ser Uncertain significance ★ ⚠ same residue
- MYO7A p.Ala2039Met Uncertain significance ★ same residue
- MYO7A p.Ala1288Pro Likely pathogenic ★★★ same type
- MYO7A p.Arg1168Gln Pathogenic ★★★ ⚠ same type
- MYO7A p.Arg1873Gln Pathogenic ★★★ ⚠ same type
- MYO7A p.Arg395Cys Likely pathogenic ★★★ ⚠ same type
- MYO7A p.Arg668Cys Pathogenic ★★★ same type
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-ala2039 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown