EYS c.5928del
Pathogenic
Multiple submitters
Classification
Pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 8.94e-05%, nfe)
Conditions
1
retinitis pigmentosa 25
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.2 | GERP 0.61, phastCons 1 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.94e-05%
European (non-Finnish) · 1/1,118,098 alleles
Overall
6.73e-05%
1/1,486,356 alleles · very rare
exomes 1/1,334,254 · genomes 0/152,102 · joint denominator
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
- Coding
- c.5928del
- MANE Select
- NM_001142800
- dbSNP
- rs2533088748
- Type
- Deletion
- Location
- chr6:64388840 (GRCh38)
- Gene constraint
- LOEUF 0.96 · pLI <0.01 (gnomAD)
Disease context
retinitis pigmentosa 25 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Retinitis pigmentosa (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive, Mitochondrial inheritance
- Onset
- Adolescent, Adult, Childhood
- Prevalence
- 1-5 / 10 000 (Europe)
Similar variants
- EYS c.1057del Pathogenic/Likely pathogenic ★★ same condition
- EYS c.5928-3_5928-1del Pathogenic/Likely pathogenic ★★ same condition
- EYS c.6079-3_6079-2del Pathogenic/Likely pathogenic ★★ same condition
- EYS c.749del Pathogenic/Likely pathogenic ★★ same condition
- EYS p.Ala1520fs Pathogenic/Likely pathogenic ★★ same condition
- EYS p.Ala1557fs Pathogenic/Likely pathogenic ★★ same condition
- EYS p.Ala2957fs Pathogenic/Likely pathogenic ★★ same condition
- EYS p.Ala3058_Tyr3059insTer 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-c-5928del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown