EPHB2 p.Ser93=
c.279G>A · rs371651342 · VCV3035904
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00878%, sas)
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 -20 | GERP -5.1 |
| Overall | ||
| CADD | 0.022 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00878%
South Asian · 8/91,076 alleles
Filtering AF
0.00519%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00474%
Overall
0.0057%
92/1,613,990 alleles · very rare
exomes 80/1,461,668 · genomes 12/152,322 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00878% | 11,385 |
| Admixed American | 0.00667% | 15,002 |
| European (non-Finnish) | 0.00636% | 15,732 |
| East Asian | 0.00446% | 22,432 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,252 |
| African / African-American | 0.00133% | 75,050 |
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.Ser93=
- Coding
- c.279G>A
- MANE Select
- NM_017449
- dbSNP
- rs371651342
- Type
- single nucleotide variant
- Location
- chr1:22784544 (GRCh38)
- Gene constraint
- LOEUF 0.265 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.41 · 5 PDB
- Residue 93
- a β-strand; the eph lbd domain
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-ser93 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown