EPHA3 p.Ala895=
c.2685C>T · rs76565471 · VCV730083
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.876%, 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 0.2 | GERP -3.2, phastCons 0.27 |
| Overall | ||
| CADD | 7.885 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.876%
East Asian · 392/44,732 alleles
Filtering AF
0.805%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.777%
Overall
0.0389%
626/1,609,856 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.876% | 114 |
| South Asian | 0.109% | 914 |
| Remaining individualsnot grpmax-eligible | 0.0706% | 1,417 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0407% | 2,457 |
| European (non-Finnish) | 0.00637% | 15,699 |
| Finnishnot grpmax-eligible | 0.00469% | 21,312 |
| Admixed American | 0.00168% | 59,600 |
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
- EPHA3
- Protein
- p.Ala895=
- Coding
- c.2685C>T
- MANE Select
- NM_005233
- dbSNP
- rs76565471
- Type
- single nucleotide variant
- Location
- chr3:89450365 (GRCh38)
- Gene constraint
- LOEUF 0.508 · pLI 0.80 (gnomAD)
- Structure
- AlphaFold pLDDT 81.22 · 28 PDB
Similar variants
- EPHA3 p.Ala895Val Uncertain significance ★ ⚠ same residue
- EPHA3 p.Ala777Gly Benign ★★ ⚠ same type
- EPHA3 p.Val597Ile Likely benign ★★ ⚠ same type
- EPHA3 p.Ala182Val Uncertain significance ★ ⚠ same type
- EPHA3 p.Ala427Val Uncertain significance ★ ⚠ same type
- EPHA3 p.Ala546Thr Uncertain significance ★ ⚠ same type
- EPHA3 p.Ala550Pro Uncertain significance ★ ⚠ same type
- EPHA3 p.Arg312Trp 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/epha3-p-ala895 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown