EYS p.Ser1376=
c.4128A>T · rs1582930506 · VCV3027806
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00733%, 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 | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.45 | |
| Overall | ||
| CADD | 4.648 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00733%
East Asian · 3/40,906 alleles
Filtering AF
0.00194%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.000193%
3/1,551,424 alleles · very rare
exomes 3/1,399,150 · genomes 0/152,274 · 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
- Protein
- p.Ser1376=
- Coding
- c.4128A>T
- MANE Select
- NM_001142800
- dbSNP
- rs1582930506
- Type
- single nucleotide variant
- Location
- chr6:64591739 (GRCh38)
- Gene constraint
- LOEUF 0.96 · pLI <0.01 (gnomAD)
Similar variants
- EYS p.Ser1376Ter Likely pathogenic ★ 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-ser1376 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown