EBF3 p.Ser229=
c.687A>C · rs1329847799 · VCV3058641
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00674%, afr)
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 -3.8 | GERP -2.7 |
| Overall | ||
| CADD | 4.367 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00674%
African / African-American · 5/74,210 alleles
Filtering AF
0.00257%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00163%
Overall
0.000315%
5/1,587,924 alleles · very rare
exomes 3/1,435,646 · genomes 2/152,278 · 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.Ser229=
- Coding
- c.687A>C
- MANE Select
- NM_001375380
- dbSNP
- rs1329847799
- Type
- single nucleotide variant
- Location
- chr10:129873546 (GRCh38)
- Gene constraint
- LOEUF 0.353 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 71.89 · 2 PDB
Similar variants
- EBF3 p.Ser229Leu Likely pathogenic ★ same residue
- 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
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-ser229 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown