EYS p.Thr676=
c.2028G>A · rs758722034 · VCV1096761
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00964%, afr)
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 -1.1 | GERP -4.3 |
| Overall | ||
| CADD | 2.704 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00964%
African / African-American · 7/72,622 alleles
Filtering AF
0.0045%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00317%
Overall
0.00318%
49/1,540,202 alleles · very rare
exomes 42/1,389,814 · genomes 7/150,388 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00964% | 10,375 |
| European (non-Finnish) | 0.00352% | 28,441 |
| Remaining individualsnot grpmax-eligible | 0.00335% | 29,860 |
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.Thr676=
- Coding
- c.2028G>A
- MANE Select
- NM_001142800
- dbSNP
- rs758722034
- Type
- single nucleotide variant
- Location
- chr6:65057723 (GRCh38)
- Gene constraint
- LOEUF 0.96 · pLI <0.01 (gnomAD)
- Residue 676
- the egf-like 7 domain
Similar variants
- EYS p.Thr676Met 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
- EYS c.5836-1G>C Pathogenic/Likely pathogenic ★★ same condition
- EYS c.6191+2T>C 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-thr676 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown