EPHB2 p.Ser805=
c.2415G>A · rs373295870 · VCV3045556
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0333%, afr)
Conditions
1
EPHB2-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 -10 | GERP -5.5 |
| Overall | ||
| CADD | 2.655 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0333%
African / African-American · 25/75,046 alleles
Filtering AF
0.0231%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0197%
Overall
0.00254%
41/1,614,200 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0333% | 3,002 |
| Admixed American | 0.00333% | 30,014 |
| South Asian | 0.00329% | 30,359 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,256 |
| East Asian | 0.00223% | 44,878 |
| European (non-Finnish) | 0.000678% | 147,505 |
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
- EPHB2
- Protein
- p.Ser805=
- Coding
- c.2415G>A
- MANE Select
- NM_017449
- dbSNP
- rs373295870
- Type
- single nucleotide variant
- Location
- chr1:22909084 (GRCh38)
- Gene constraint
- LOEUF 0.265 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.41 · 5 PDB
- Residue 805
- the protein kinase domain; an α-helix
Disease context
EPHB2-related disorder
Similar variants
- EPHB2 p.Tyr240Asp Uncertain significance ⚠ same condition
- EPHB2 c.968-7G>A Likely benign same condition
- EPHB2 c.*120G>A Likely benign same condition
- EPHB2 c.*213A>G Likely benign same condition
- EPHB2 c.*291C>T Likely benign same condition
- EPHB2 p.Asn755= Likely benign same condition
- EPHB2 p.His583= Likely benign same condition
- EPHB2 p.Phe803= Likely 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/ephb2-p-ser805 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown