MYO7A p.Pro1556=
c.4668G>A · rs376892582 · VCV745415
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.188%, afr)
Conditions
2
Inborn genetic diseases
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 0.26 | GERP -0.81, phastCons 0.95 |
| Overall | ||
| CADD | 11.85 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.188%
African / African-American · 141/75,026 alleles
Filtering AF
0.163%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.153%
Overall
0.012%
194/1,610,882 alleles · rare
exomes 111/1,458,544 · genomes 83/152,338 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.188% | 532 |
| Middle Eastern | 0.0331% | 3,023 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,198 |
| Admixed American | 0.0168% | 5,970 |
| European (non-Finnish) | 0.00237% | 42,111 |
| South Asian | 0.00111% | 90,328 |
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.Pro1556=
- Coding
- c.4668G>A
- MANE Select
- NM_000260
- dbSNP
- rs376892582
- Type
- single nucleotide variant
- Location
- chr11:77199634 (GRCh38)
- Gene constraint
- LOEUF 0.995 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.73 · 1 PDB
- Residue 1556
- the ferm 1 domain
Similar variants
- MYO7A p.Pro1556Leu Conflicting classifications of pathogenicity ★ ⚠ 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-pro1556 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown