EPS8 p.Ser60=
c.180A>G · VCV3711898
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0581%, eas)
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 -2.6 | GERP -4.7 |
| Overall | ||
| CADD | 5.046 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0581%
East Asian · 26/44,780 alleles
Filtering AF
0.0406%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0348%
Overall
0.0031%
50/1,612,274 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0581% | 1,722 |
| South Asian | 0.0154% | 6,494 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,916 |
| Finnishnot grpmax-eligible | 0.00156% | 64,004 |
| European (non-Finnish) | 0.00017% | 589,338 |
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
- EPS8
- Protein
- p.Ser60=
- Coding
- c.180A>G
- MANE Select
- NM_004447
- Type
- single nucleotide variant
- Location
- chr12:15670880 (GRCh38)
- Gene constraint
- LOEUF 0.443 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 70.77 · 2 PDB
Similar variants
- EPS8 p.Ser60Ter Pathogenic ★ same residue
- EPS8 c.205-8A>G Uncertain significance ★★ same type
- EPS8 p.Ala150Val Uncertain significance ★★ ⚠ same type
- EPS8 p.Ala219Val Uncertain significance ★★ ⚠ same type
- EPS8 p.Ala416Asp Uncertain significance ★★ ⚠ same type
- EPS8 p.Arg195Trp Uncertain significance ★★ ⚠ same type
- EPS8 p.Arg403Trp Uncertain significance ★★ ⚠ same type
- EPS8 p.Arg432Gln Uncertain significance ★★ ⚠ 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/eps8-p-ser60 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown