EYS p.Gln1925=
c.5775A>G · rs1465801209 · VCV965378
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0458%, eas)
Conditions
2
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 0.64 | GERP 0.048, phastCons 0.56 |
| Overall | ||
| CADD | 1.727 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0458%
East Asian · 17/37,078 alleles
Filtering AF
0.0292%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.024%
Overall
0.00128%
19/1,487,900 alleles · ultra-rare
exomes 14/1,336,108 · genomes 5/151,792 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0458% | 2,181 |
| Admixed American | 0.00495% | 20,185 |
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.Gln1925=
- Coding
- c.5775A>G
- MANE Select
- NM_001142800
- dbSNP
- rs1465801209
- Type
- single nucleotide variant
- Location
- chr6:64439222 (GRCh38)
- Gene constraint
- LOEUF 0.96 · pLI <0.01 (gnomAD)
- Residue 1925
- the laminin g-like 1 domain
Similar variants
- EYS c.1056+1G>A Pathogenic/Likely pathogenic ★★ same condition
- EYS c.1056+3A>C Likely pathogenic ★★ same condition
- EYS c.1057-1G>A Likely pathogenic ★★ same condition
- EYS c.1184+1G>A Pathogenic/Likely pathogenic ★★ same condition
- EYS c.1184+1G>T Likely pathogenic ★★ same condition
- EYS c.1185-1G>A Likely pathogenic ★★ same condition
- EYS c.1299+1G>T Pathogenic/Likely pathogenic ★★ same condition
- EYS c.1299+2T>A 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-gln1925 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown