EPHA3 p.Arg883=
c.2649G>A · rs145084709 · VCV3035334
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.451%, afr)
Conditions
1
EPHA3-related disorder
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 4.6 | GERP 0.17, phastCons 1 |
| Overall | ||
| CADD | 8.684 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.451%
African / African-American · 338/75,012 alleles
Filtering AF
0.411%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.396%
Overall
0.0229%
369/1,613,584 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.451% | 222 |
| Remaining individualsnot grpmax-eligible | 0.0288% | 3,472 |
| Admixed American | 0.0184% | 5,448 |
| European (non-Finnish) | 0.00017% | 589,901 |
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.Arg883=
- Coding
- c.2649G>A
- MANE Select
- NM_005233
- dbSNP
- rs145084709
- Type
- single nucleotide variant
- Location
- chr3:89450329 (GRCh38)
- Gene constraint
- LOEUF 0.508 · pLI 0.80 (gnomAD)
- Structure
- AlphaFold pLDDT 81.22 · 28 PDB
- Residue 883
- an α-helix
Disease context
EPHA3-related disorder
Similar variants
- EPHA3 c.1432-7C>T Likely benign same condition
- EPHA3 p.Asn907= Benign same condition
- EPHA3 p.Glu298Gln Likely benign ⚠ same condition
- EPHA3 p.Gly934= Benign same condition
- EPHA3 p.Ile648= Likely benign same condition
- EPHA3 p.Leu281= Likely benign same condition
- EPHA3 p.Lys713Thr Likely benign ⚠ same condition
- EPHA3 p.Lys800= Benign 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/epha3-p-arg883 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown