MYO7A p.Lys896=
c.2688G>A · rs782192254 · VCV1123692
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0183%, amr)
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 1.7 | GERP 0.56, phastCons 1 |
| Overall | ||
| CADD | 9.335 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0183%
Admixed American · 11/59,982 alleles
Filtering AF
0.0102%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00786%
Overall
0.000869%
14/1,611,958 alleles · ultra-rare
exomes 12/1,459,710 · genomes 2/152,248 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0183% | 5,453 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,426 |
| European (non-Finnish) | 0.00017% | 589,797 |
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.Lys896=
- Coding
- c.2688G>A
- MANE Select
- NM_000260
- dbSNP
- rs782192254
- Type
- single nucleotide variant
- Location
- chr11:77180475 (GRCh38)
- Gene constraint
- LOEUF 0.995 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.73 · 1 PDB
- Residue 896
- the 'sah' region
Similar variants
- 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
- MYO7A p.Gly2187Asp 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-lys896 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown