EBF3 c.554+1del
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
canonical splice-site (±1/±2)
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | canonical splice-site (±1/±2) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| Splicing | ||
| Splice region | donor +1 | canonical splice dinucleotide (donor +1) · inside the BP7-excluded zone |
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 2.4, phastCons 1 |
| Non-coding constraint | Z 2.32 | 1 kb window · o/e 0.82 · regional · uncalibrated |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- EBF3
- Coding
- c.554+1del
- MANE Select
- NM_001375380
- Type
- Deletion
- Location
- chr10:129957257 (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 p.Asn40fs Likely pathogenic ★ same type
- EBF3 p.Asp222fs Likely pathogenic ★ same type
- EBF3 p.Gln113fs 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-c-554-plus-1del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown