EPHB3 p.Lys943=
c.2829G>A · rs372198999 · VCV2654327
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.298%, mid)
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 -0.14, phastCons 1 |
| Overall | ||
| CADD | 4.711 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.298%
Middle Eastern · 18/6,042 alleles
Filtering AF
0.193%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.159%
Overall
0.0267%
429/1,609,734 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.298% | 336 |
| Admixed American | 0.1% | 996 |
| South Asian | 0.081% | 1,235 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0684% | 1,461 |
| Remaining individualsnot grpmax-eligible | 0.0481% | 2,078 |
| European (non-Finnish) | 0.0191% | 5,234 |
| African / African-American | 0.004% | 24,993 |
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
- EPHB3
- Protein
- p.Lys943=
- Coding
- c.2829G>A
- MANE Select
- NM_004443
- dbSNP
- rs372198999
- Type
- single nucleotide variant
- Location
- chr3:184581349 (GRCh38)
- Gene constraint
- LOEUF 0.435 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 82.62 · 4 PDB
- Residue 943
- the sam domain
Similar variants
- EPHB3 c.1748+4C>T Benign ★★ same type
- EPHB3 p.Phe689= Benign ★★ same type
- EPHB3 p.Pro438= Benign ★★ same type
- EPHB3 p.Ala220Thr Uncertain significance ★ ⚠ same type
- EPHB3 p.Ala229Val Uncertain significance ★ ⚠ same type
- EPHB3 p.Ala315Thr Uncertain significance ★ ⚠ same type
- EPHB3 p.Ala332Val Uncertain significance ★ ⚠ same type
- EPHB3 p.Ala442Glu 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/ephb3-p-lys943 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown