EPHB2 p.Gln722Ter
c.2164C>T · rs121912582 · VCV8532
Pathogenic
No assertion criteria
Classification
Pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
prostate cancer/brain cancer susceptibility
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 12 of 16 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 2.7, phastCons 1 |
| Overall | ||
| CADD | 45.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- EPHB2
- Protein
- p.Gln722Ter
- Coding
- c.2164C>T
- MANE Select
- NM_017449
- dbSNP
- rs121912582
- Type
- single nucleotide variant
- Location
- chr1:22907980 (GRCh38)
- Gene constraint
- LOEUF 0.265 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.41 · 5 PDB
- Residue 722
- the protein kinase domain; an α-helix
Similar variants
- EPHB2 p.Ala279Ser Benign ★★ same condition
- EPHB2 p.Asp678Asn Likely benign ★★ ⚠ same condition
- EPHB2 c.*214_*215del Uncertain significance ★ same condition
- EPHB2 p.Val414Ile Uncertain significance ★★ ⚠ same type
- EPHB2 c.1766-9G>T Benign/Likely benign ★★ same type
- EPHB2 p.Asn242= Likely benign ★★ same type
- EPHB2 p.Asp574= Benign ★★ same type
- EPHB2 p.Gln875= Benign ★★ 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/ephb2-p-gln722ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown