EPHB1 p.Thr981=
c.2943G>A · rs16842880 · VCV782434
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.38%, afr)
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 -4.1 | GERP -5.7 |
| Overall | ||
| CADD | 1.689 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.38%
African / African-American · 3,284/74,922 alleles
Filtering AF
4.26%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.21%
Overall
0.227%
3,654/1,607,914 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.38% | 23 |
| Remaining individualsnot grpmax-eligible | 0.257% | 390 |
| Admixed American | 0.226% | 442 |
| Middle Eastern | 0.165% | 606 |
| South Asian | 0.0168% | 5,947 |
| European (non-Finnish) | 0.00433% | 23,083 |
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.Thr981=
- Coding
- c.2943G>A
- MANE Select
- NM_004441
- dbSNP
- rs16842880
- Type
- single nucleotide variant
- Location
- chr3:135259108 (GRCh38)
- Gene constraint
- LOEUF 0.441 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 83.95 · 8 PDB
- Residue 981
- a UniProt-annotated variant site (in)
Similar variants
- EPHB1 p.Ile561= Benign ★★ same type
- EPHB1 p.Phe552= Benign/Likely 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
- EPHB1 p.Ala39Val Uncertain significance ★ ⚠ same type
- EPHB1 p.Ala547Val 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-thr981 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown