EBF3 p.Ile400=
c.1200C>A · rs969027167 · VCV3030072
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0012%, nfe)
Conditions
1
EBF3-related disorder
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 8.4 | GERP 0.58, phastCons 1 |
| Overall | ||
| CADD | 12.63 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0012%
European (non-Finnish) · 14/1,164,164 alleles
Filtering AF
0.000698%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000546%
Overall
0.000883%
14/1,585,764 alleles · very rare
exomes 12/1,433,682 · genomes 2/152,082 · joint denominator
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
- EBF3
- Protein
- p.Ile400=
- Coding
- c.1200C>A
- MANE Select
- NM_001375380
- dbSNP
- rs969027167
- Type
- single nucleotide variant
- Location
- chr10:129842288 (GRCh38)
- Gene constraint
- LOEUF 0.353 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 71.89 · 2 PDB
- Residue 400
- an α-helix
Similar variants
- EBF3 p.Arg404Ter Pathogenic/Likely pathogenic ★★ same condition
- EBF3 c.1194+1G>C Likely pathogenic ★ same condition
- EBF3 p.Arg163Pro Likely pathogenic ★ same condition
- EBF3 p.Cys161Arg Likely pathogenic ★ same condition
- EBF3 p.Met232Lys Likely pathogenic ★ same condition
- EBF3 p.Val82Met Uncertain significance ★ ⚠ same condition
- EBF3 c.1373-10A>G Likely benign same condition
- EBF3 c.412-7C>T Likely benign 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/ebf3-p-ile400 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown