EBF3 p.Arg163=
c.489G>T · rs377458707 · VCV3030150
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.104%, 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 | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.59 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 13.09 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.104%
African / African-American · 78/74,800 alleles
Filtering AF
0.0856%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0787%
Overall
0.00535%
86/1,608,628 alleles · rare
exomes 45/1,456,506 · genomes 41/152,122 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.104% | 959 |
| Remaining individualsnot grpmax-eligible | 0.00644% | 15,535 |
| South Asian | 0.00332% | 30,125 |
| Admixed American | 0.00167% | 59,896 |
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.Arg163=
- Coding
- c.489G>T
- MANE Select
- NM_001375380
- dbSNP
- rs377458707
- Type
- single nucleotide variant
- Location
- chr10:129957323 (GRCh38)
- Gene constraint
- LOEUF 0.353 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 71.89 · 2 PDB
- Residue 163
- a UniProt-annotated variant site (in hadds; partial loss of transcriptional activator activity); a UniProt-annotated variant site (in hadds; loss of transcriptional activator activity); a functional site (interaction with dna)
Similar variants
- EBF3 p.Arg163Pro Likely pathogenic ★ same residue
- EBF3 p.Arg163Gln Pathogenic ★★ same residue
- EBF3 p.Arg163Leu Pathogenic ★★ same residue
- EBF3 p.Arg163Trp Pathogenic/Likely pathogenic ★★ same residue
- EBF3 p.Arg163Gly Likely pathogenic same residue
- EBF3 p.Arg404Ter Pathogenic/Likely pathogenic ★★ same condition
- EBF3 c.1194+1G>C Likely pathogenic ★ same condition
- EBF3 p.Cys161Arg Likely 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/ebf3-p-arg163 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown