AEBP1 p.Phe475=
c.1425C>T · VCV3697851
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.0021%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.22 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.2 | GERP -2.8 |
| Overall | ||
| CADD | 16.52 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0021%
Admixed American · 1/47,670 alleles
Filtering AF
0.000256%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000165%
Overall
0.00059%
9/1,525,592 alleles · very rare
exomes 9/1,373,254 · genomes 0/152,338 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0021% | 47,670 |
| South Asian | 0.00131% | 76,322 |
| European (non-Finnish) | 0.000616% | 162,250 |
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
- AEBP1
- Protein
- p.Phe475=
- Coding
- c.1425C>T
- MANE Select
- NM_001129
- Type
- single nucleotide variant
- Location
- chr7:44110749 (GRCh38)
- Gene constraint
- LOEUF 0.735 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.99
- Residue 475
- the f5/8 type c domain; the 'required for dna-binding and interaction with nfkbia' region; the 'interaction with mapk1 and mapk3' region
Similar variants
- AEBP1 c.1018+1G>A Likely pathogenic ★★ same type
- AEBP1 c.1630+1G>A Pathogenic ★★ same type
- AEBP1 c.1630+2T>A Pathogenic ★★ same type
- AEBP1 p.Arg595Ter Pathogenic ★★ same type
- AEBP1 p.Cys581Ter Pathogenic/Likely pathogenic ★★ same type
- AEBP1 p.Cys868Ter Likely pathogenic ★★ same type
- AEBP1 p.Gln781Ter Pathogenic/Likely pathogenic ★★ same type
- AEBP1 p.Tyr428Ter Pathogenic/Likely pathogenic ★★ 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/aebp1-p-phe475 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown