EBP p.Ile112=
c.336C>T · rs905580892 · VCV766137
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00217%, amr)
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 2.1 | GERP 1.1, phastCons 0.99 |
| Overall | ||
| CADD | 16.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00217%
Admixed American · 1/46,031 alleles
Overall
0.000273%
3/1,098,111 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00217% | 46,031 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,648 |
| European (non-Finnish) | 0.000112% | 895,399 |
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
- EBP
- Protein
- p.Ile112=
- Coding
- c.336C>T
- MANE Select
- NM_001378122 · reported on NM_006579
- dbSNP
- rs905580892
- Type
- single nucleotide variant
- Location
- chrX:48527023 (GRCh38)
- Structure
- AlphaFold pLDDT 59.09
- Residue 112
- the 'disordered' region
Similar variants
- EBP p.Arg110Gln Pathogenic/Likely pathogenic ★★ same type
- EBP p.Arg110Ter Pathogenic ★★ same type
- EBP p.Arg147Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- EBP p.Arg147His Pathogenic ★★ ⚠ same type
- EBP p.Arg62Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
- EBP p.Glu80Lys Pathogenic/Likely pathogenic ★★ same type
- EBP p.Gly161Arg Likely pathogenic ★★ same type
- EBP p.Ser98Phe 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/ebp-p-ile112 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown