EYS p.Phe2358=
c.7074T>C · rs1772620298 · VCV1546737
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00978%, eas)
Conditions
1
inherited retinal dystrophy
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.031 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 0.61 | GERP -2.4, phastCons 0.96 |
| Overall | ||
| CADD | 3.977 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00978%
East Asian · 4/40,906 alleles
Filtering AF
0.00328%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00193%
Overall
0.000323%
5/1,550,284 alleles · very rare
exomes 5/1,397,948 · genomes 0/152,336 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00978% | 10,226 |
| Remaining individualsnot grpmax-eligible | 0.00166% | 60,112 |
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.Phe2358=
- Coding
- c.7074T>C
- MANE Select
- NM_001142800
- dbSNP
- rs1772620298
- Type
- single nucleotide variant
- Location
- chr6:63864340 (GRCh38)
- Gene constraint
- LOEUF 0.96 · pLI <0.01 (gnomAD)
- Residue 2358
- the egf-like 22 domain
Similar variants
- 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
- EYS c.5836-1G>C Pathogenic/Likely pathogenic ★★ same condition
- EYS c.6191+2T>C Likely pathogenic ★★ same condition
- EYS c.7228+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-phe2358 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown