EBP p.Leu48=
c.144G>A · rs1179635332 · VCV1992824
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00296%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.50 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP -1.4, phastCons 1 |
| Overall | ||
| CADD | 6.419 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00296%
East Asian · 1/33,832 alleles
Filtering AF
0.000241%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000158%
Overall
0.000637%
7/1,098,267 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00296% | 33,832 |
| European (non-Finnish) | 0.00067% | 149,258 |
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.Leu48=
- Coding
- c.144G>A
- MANE Select
- NM_001378122 · reported on NM_006579
- dbSNP
- rs1179635332
- Type
- single nucleotide variant
- Location
- chrX:48523915 (GRCh38)
- Structure
- AlphaFold pLDDT 59.09
- Residue 48
- 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-leu48 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown