EPHB1 p.Ile837=
c.2511C>T · rs143367042 · VCV69746
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0506%, 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 -5.2 | GERP -5.7 |
| Overall | ||
| CADD | 1.761 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0506%
Middle Eastern · 3/5,926 alleles
Filtering AF
0.0137%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00903%
Overall
0.00952%
151/1,586,242 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0506% | 1,975 |
| European (non-Finnish) | 0.0112% | 8,922 |
| African / African-American | 0.00941% | 10,631 |
| Remaining individualsnot grpmax-eligible | 0.00818% | 12,226 |
| South Asian | 0.00451% | 22,190 |
| East Asian | 0.00226% | 44,234 |
| Finnishnot grpmax-eligible | 0.00157% | 63,576 |
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
- EPHB1
- Protein
- p.Ile837=
- Coding
- c.2511C>T
- MANE Select
- NM_004441
- dbSNP
- rs143367042
- Type
- single nucleotide variant
- Location
- chr3:135248330 (GRCh38)
- Gene constraint
- LOEUF 0.441 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 83.95 · 8 PDB
- Residue 837
- an α-helix; the protein kinase domain
Similar variants
- EPHB1 p.Ile837Met Uncertain significance ★ ⚠ same residue
- EPHB1 p.Ile561= Benign ★★ same type
- EPHB1 p.Phe552= Benign/Likely benign ★★ same type
- EPHB1 p.Thr981= Benign ★★ same type
- EPHB1 c.2347-1G>A Uncertain significance ★ same type
- EPHB1 p.Ala12Ser Uncertain significance ★ ⚠ same type
- EPHB1 p.Ala132Gly Uncertain significance ★ ⚠ same type
- EPHB1 p.Ala182Thr 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/ephb1-p-ile837 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown