EBP p.Val43=
c.129C>T · rs782150594 · VCV725573
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00603%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.20 | acceptor loss · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.8 | GERP -4.1 |
| Overall | ||
| CADD | 2.045 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00603%
European (non-Finnish) · 54/895,086 alleles
Filtering AF
0.00473%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00423%
Overall
0.00463%
56/1,209,040 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00603% | 16,576 |
| Finnishnot grpmax-eligible | 0.00215% | 46,424 |
| African / African-American | 0.00176% | 56,807 |
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.Val43=
- Coding
- c.129C>T
- MANE Select
- NM_001378122 · reported on NM_006579
- dbSNP
- rs782150594
- Type
- single nucleotide variant
- Location
- chrX:48523900 (GRCh38)
- Structure
- AlphaFold pLDDT 59.09
- Residue 43
- the 'disordered' region
Similar variants
- EBP p.Val43fs Pathogenic ★ same residue
- PRSS48 p.Val43fs Uncertain significance same residue
- 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
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-val43 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown