EBF3 p.Lys558fs
c.1674del · VCV3770078
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 15 of 17 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 9.8 | GERP 2.9, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- EBF3
- Protein
- p.Lys558fs
- Coding
- c.1674del
- MANE Select
- NM_001375380
- Type
- Deletion
- Location
- chr10:129840330 (GRCh38)
- Gene constraint
- LOEUF 0.353 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 71.89 · 2 PDB
Similar variants
- EBF3 c.485+2_485+8del Pathogenic/Likely pathogenic ★★ same type
- EBF3 p.Thr477fs Pathogenic ★★ same type
- EBF3 c.1561+3_1561+6del Likely pathogenic ★ same type
- EBF3 c.289_291+1del Pathogenic ★ same type
- EBF3 c.291+2del Pathogenic ★ same type
- EBF3 c.554+1del Likely pathogenic ★ same type
- EBF3 p.Asn40fs Likely pathogenic ★ same type
- EBF3 p.Asp222fs 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-lys558fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown