MYO7A p.Gln1097=
c.3291G>A · rs561459113 · VCV726085
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.111%, afr)
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 · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.4 | GERP 0.47, phastCons 1 |
| Overall | ||
| CADD | 9.347 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.111%
African / African-American · 81/73,188 alleles
Filtering AF
0.0912%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.084%
Overall
0.00548%
85/1,551,244 alleles · rare
exomes 33/1,398,888 · genomes 52/152,356 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.111% | 904 |
| Remaining individualsnot grpmax-eligible | 0.00499% | 20,039 |
| Admixed American | 0.00196% | 51,028 |
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.Gln1097=
- Coding
- c.3291G>A
- MANE Select
- NM_000260
- dbSNP
- rs561459113
- Type
- single nucleotide variant
- Location
- chr11:77183073 (GRCh38)
- Gene constraint
- LOEUF 0.995 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.73 · 1 PDB
- Residue 1097
- the myth4 1 domain
Similar variants
- MYO7A p.Gln1097Ter Pathogenic/Likely pathogenic ★★ same residue
- MYO7A p.Ala1288Pro Likely pathogenic ★★★ same condition
- MYO7A p.Arg1168Gln Pathogenic ★★★ ⚠ same condition
- MYO7A p.Arg1873Gln Pathogenic ★★★ ⚠ same condition
- MYO7A p.Arg395Cys Likely pathogenic ★★★ ⚠ same condition
- MYO7A p.Arg668Cys Pathogenic ★★★ same condition
- MYO7A p.Arg853His Likely pathogenic ★★★ same condition
- MYO7A p.Glu968Asp 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-gln1097 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown