EBP p.Leu128=
c.382C>T · rs142881014 · VCV158547
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 -0.23 | GERP -4.1 |
| Overall | ||
| CADD | 4.083 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Ashkenazi Jewishnot grpmax-eligible | 0.79% | 127 |
| African / African-Americangrpmax | 0.684% | 146 |
| Middle Eastern | 0.597% | 167 |
| Admixed American | 0.397% | 252 |
| Remaining individualsnot grpmax-eligible | 0.363% | 275 |
| European (non-Finnish) | 0.0689% | 1,451 |
| South Asian | 0.00528% | 18,924 |
Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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.Leu128=
- Coding
- c.382C>T
- MANE Select
- NM_001378122 · reported on NM_006579
- dbSNP
- rs142881014
- Type
- single nucleotide variant
- Location
- chrX:48527198 (GRCh38)
- Structure
- AlphaFold pLDDT 59.09
- Residue 128
- the 'disordered' region
Disease context
X-linked chondrodysplasia punctata 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor X-linked dominant chondrodysplasia punctata (Orphanet):
- Inheritance
- X-linked dominant
- Onset
- Antenatal, Infancy, Neonatal
- Prevalence
- 1-9 / 1 000 000 (Europe)
Similar variants
- EBP p.Leu128Pro Likely pathogenic ★ same residue
- EBP p.Leu128Arg Uncertain significance ★ ⚠ same residue
- EBP p.Arg110Gln Pathogenic/Likely pathogenic ★★ same condition
- EBP p.Arg110Ter Pathogenic ★★ same condition
- EBP p.Arg147His Pathogenic ★★ ⚠ same condition
- EBP p.Arg62Trp Pathogenic/Likely pathogenic ★★ ⚠ same condition
- EBP p.Glu80Lys Pathogenic/Likely pathogenic ★★ same condition
- EBP p.Gly161Arg Likely pathogenic ★★ same condition
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-leu128 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown