EBF3 p.Ser442del
c.1321AGC[1] · rs1298189712 · VCV3068910
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.6, phastCons 1 |
| Overall | ||
| CADD | 19.78 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,012 alleles
Overall
0.000124%
2/1,614,142 alleles · very rare
exomes 1/1,461,890 · genomes 1/152,252 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 60,012 |
| African / African-American | 0.00133% | 74,954 |
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.Ser442del
- Coding
- c.1321AGC[1]
- MANE Select
- NM_001375380
- dbSNP
- rs1298189712
- Type
- Microsatellite
- Location
- chr10:129842162 (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.Asn237del Pathogenic ★ same type
- EBF3 p.Glu175fs Pathogenic ★ same type
- EBF3 p.His395fs Likely pathogenic ★ same type
- EBF3 p.Leu154fs Likely pathogenic ★ same type
- EBF3 p.Lys97fs Pathogenic ★ same type
- EBF3 p.Phe186_Phe187insTer Pathogenic ★ same type
- EBF3 p.Thr485fs 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/ebf3-p-ser442del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown