EBP p.Ile138=
c.414C>T · rs976210101 · VCV759959
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00218%, amr)
Conditions
2
MEND syndrome
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 -5.4 | GERP -4.2 |
| Overall | ||
| CADD | 1.176 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00218%
Admixed American · 1/45,975 alleles
Filtering AF
0.000325%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000209%
Overall
0.00082%
9/1,098,195 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00218% | 45,975 |
| African / African-American | 0.00174% | 57,629 |
| European (non-Finnish) | 0.000782% | 127,914 |
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.Ile138=
- Coding
- c.414C>T
- MANE Select
- NM_001378122 · reported on NM_006579
- dbSNP
- rs976210101
- Type
- single nucleotide variant
- Location
- chrX:48527230 (GRCh38)
- Structure
- AlphaFold pLDDT 59.09
- Residue 138
- the 'disordered' region
Similar variants
- EBP p.Arg110Gln Pathogenic/Likely pathogenic ★★ same condition
- EBP p.Arg110Ter Pathogenic ★★ same condition
- EBP p.Arg147Cys Pathogenic/Likely 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.Trp186Ter 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-ile138 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown