EBP p.Trp186Ter
c.558G>A · VCV4710748
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen); NMD-escape possible for C-terminal truncations |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.1, phastCons 1 |
| Overall | ||
| CADD | 37.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- EBP
- Protein
- p.Trp186Ter
- Coding
- c.558G>A
- MANE Select
- NM_001378122 · reported on NM_006579
- Type
- single nucleotide variant
- Location
- chrX:48528322 (GRCh38)
- Structure
- AlphaFold pLDDT 59.09
- Residue 186
- 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.Trp186Arg 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
- EBP p.Trp61Ter Pathogenic/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-trp186ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown