EYA1 p.Pro9=
c.27G>A · rs763352962 · VCV1630322
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.033%, mid)
Conditions
1
branchio-oto-renal syndrome
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 1.4 | GERP 0.78, phastCons 1 |
| Overall | ||
| CADD | 12.86 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.033%
Middle Eastern · 2/6,054 alleles
Filtering AF
0.00583%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00242%
Overall
0.00143%
23/1,613,290 alleles · ultra-rare
exomes 23/1,461,038 · genomes 0/152,252 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.033% | 3,027 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,611 |
| South Asian | 0.00439% | 22,766 |
| Admixed American | 0.00167% | 59,984 |
| European (non-Finnish) | 0.00102% | 98,286 |
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
- EYA1
- Protein
- p.Pro9=
- Coding
- c.27G>A
- MANE Select
- NM_000503
- dbSNP
- rs763352962
- Type
- single nucleotide variant
- Location
- chr8:71354879 (GRCh38)
- Gene constraint
- LOEUF 0.291 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 66.68
- Residue 9
- the 'disordered' region
Similar variants
- EYA1 p.Pro9Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- EYA1 c.1050+1G>T Pathogenic ★★ same condition
- EYA1 c.1051-2A>G Pathogenic ★★ same condition
- EYA1 c.1199+1G>A Pathogenic/Likely pathogenic ★★ same condition
- EYA1 c.1200-1G>A Pathogenic ★★ same condition
- EYA1 c.1360+5G>A Pathogenic/Likely pathogenic ★★ same condition
- EYA1 c.1361-1G>A Pathogenic ★★ same condition
- EYA1 c.1597+1G>A Pathogenic/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/eya1-p-pro9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown