EYS p.Ser1367=
c.4101G>A · rs1358175561 · VCV1606366
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00548%, afr)
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 0.35 | |
| Overall | ||
| CADD | 4.772 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00548%
African / African-American · 4/72,966 alleles
Filtering AF
0.00178%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00106%
Overall
0.00116%
18/1,551,102 alleles · very rare
exomes 15/1,399,086 · genomes 3/152,016 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00548% | 18,241 |
| South Asian | 0.00357% | 28,017 |
| Remaining individualsnot grpmax-eligible | 0.00166% | 60,084 |
| European (non-Finnish) | 0.000872% | 114,673 |
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.Ser1367=
- Coding
- c.4101G>A
- MANE Select
- NM_001142800
- dbSNP
- rs1358175561
- Type
- single nucleotide variant
- Location
- chr6:64591766 (GRCh38)
- Gene constraint
- LOEUF 0.96 · pLI <0.01 (gnomAD)
Similar variants
- EYS p.Ser1367Leu Uncertain significance ★★ same residue
- EYS p.Ser1367Pro Uncertain significance ★★ same residue
- EYS p.Ser1367Ter Likely pathogenic ★ same residue
- EYS c.1056+1G>A Pathogenic/Likely pathogenic ★★ same type
- EYS c.1056+3A>C Likely pathogenic ★★ same type
- EYS c.1057-1G>A Likely pathogenic ★★ same type
- EYS c.1184+1G>A Pathogenic/Likely pathogenic ★★ same type
- EYS c.1184+1G>T Likely pathogenic ★★ same type
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-ser1367 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown