EYS p.Asp1139=
c.3417T>C · rs1238692406 · VCV792717
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.34 | GERP -0.98 |
| Overall | ||
| CADD | 1.205 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- EYS
- Protein
- p.Asp1139=
- Coding
- c.3417T>C
- MANE Select
- NM_001142800
- dbSNP
- rs1238692406
- Type
- single nucleotide variant
- Location
- chr6:64813404 (GRCh38)
- Gene constraint
- LOEUF 0.96 · pLI <0.01 (gnomAD)
- Residue 1139
- the egf-like 19 domain
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.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+2T>A Likely pathogenic ★★ same condition
- EYS c.1599+1G>T 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-asp1139 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown