MYO7A p.Ser1829=
c.5487C>T · rs397516318 · VCV43284
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0332%, mid)
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 |
|---|---|---|
| Pangolin | Δ0.24 | loss · gain 0.04 · SpliceAI below 0.2 · independent |
| Constraint at this position | ||
| Conservation | phyloP -6 | GERP -2.5 |
| Overall | ||
| CADD | 7.684 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0332%
Middle Eastern · 2/6,030 alleles
Filtering AF
0.00585%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00243%
Overall
0.00121%
19/1,568,190 alleles · ultra-rare
exomes 18/1,416,026 · genomes 1/152,164 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0332% | 3,015 |
| Admixed American | 0.00188% | 53,324 |
| European (non-Finnish) | 0.0013% | 77,135 |
| South Asian | 0.00117% | 85,188 |
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.Ser1829=
- Coding
- c.5487C>T
- MANE Select
- NM_000260
- dbSNP
- rs397516318
- Type
- single nucleotide variant
- Location
- chr11:77205468 (GRCh38)
- Gene constraint
- LOEUF 0.995 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.73 · 1 PDB
- Residue 1829
- the myth4 2 domain; an α-helix
Similar variants
- MYO7A p.Ser1829Arg Uncertain significance ★ ⚠ same residue
- MYO7A p.Ser1829Ile 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
- MYO7A p.Arg853His Likely 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-ser1829 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown