EYS p.Asp643=
c.1929T>C · rs1412901872 · VCV1136057
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.044%, eas)
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 -3.1, phastCons 0.003 |
| Overall | ||
| CADD | 2.24 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.044%
East Asian · 18/40,912 alleles
Filtering AF
0.0284%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0234%
Overall
0.00129%
20/1,551,092 alleles · ultra-rare
exomes 19/1,399,130 · genomes 1/151,962 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.044% | 2,273 |
| European (non-Finnish) | 0.000174% | 573,273 |
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.Asp643=
- Coding
- c.1929T>C
- MANE Select
- NM_001142800
- dbSNP
- rs1412901872
- Type
- single nucleotide variant
- Location
- chr6:65295957 (GRCh38)
- Gene constraint
- LOEUF 0.96 · pLI <0.01 (gnomAD)
- Residue 643
- the egf-like 7 domain
Similar variants
- EYS p.Asp643Tyr 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-asp643 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown