EYS p.Pro859=
c.2577T>C · rs1265766894 · VCV1100409
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0334%, mid)
Conditions
1
inherited retinal dystrophy
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 3.7 | phastCons 1 |
| Overall | ||
| CADD | 6.287 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0334%
Middle Eastern · 2/5,992 alleles
Filtering AF
0.00635%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00434%
Overall
0.00116%
18/1,551,296 alleles · ultra-rare
exomes 18/1,399,040 · genomes 0/152,256 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0334% | 2,996 |
| East Asian | 0.0147% | 6,818 |
| Remaining individualsnot grpmax-eligible | 0.00666% | 15,026 |
| European (non-Finnish) | 0.000523% | 191,109 |
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
- EYS
- Protein
- p.Pro859=
- Coding
- c.2577T>C
- MANE Select
- NM_001142800
- dbSNP
- rs1265766894
- Type
- single nucleotide variant
- Location
- chr6:64912548 (GRCh38)
- Gene constraint
- LOEUF 0.96 · pLI <0.01 (gnomAD)
- Residue 859
- the egf-like 12 domain
Similar variants
- EYS p.Pro859Ala Uncertain significance ★ same residue
- EYS p.Pro859Leu Uncertain significance ★ same residue
- EYS p.Pro859Thr Uncertain significance ★ same residue
- EYS c.1056+1G>A Pathogenic/Likely pathogenic ★★ same condition
- EYS c.1299+1G>T Pathogenic/Likely pathogenic ★★ same condition
- EYS c.1766+1G>T Pathogenic/Likely pathogenic ★★ same condition
- EYS c.2259+1G>A Pathogenic/Likely pathogenic ★★ same condition
- EYS c.3243+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/eys-p-pro859 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown