EPHB2 p.Asn755=
c.2265C>T · rs141476431 · VCV3036596
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.012%, 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 0.62 | GERP -0.57, phastCons 0.99 |
| Overall | ||
| CADD | 10.55 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.012%
African / African-American · 9/74,944 alleles
Filtering AF
0.00623%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00467%
Overall
0.000681%
11/1,614,142 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.012% | 8,327 |
| South Asian | 0.0011% | 91,092 |
| European (non-Finnish) | 8.47e-05% | 1,180,054 |
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.Asn755=
- Coding
- c.2265C>T
- MANE Select
- NM_017449
- dbSNP
- rs141476431
- Type
- single nucleotide variant
- Location
- chr1:22908081 (GRCh38)
- Gene constraint
- LOEUF 0.265 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.41 · 5 PDB
- Residue 755
- the protein kinase 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.His583= Likely benign same condition
- EPHB2 p.Phe803= Likely benign same condition
- EPHB2 p.Ser218= 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-asn755 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown