UBE3A p.Phe802fs
c.2403_2404del · VCV4823694
Likely pathogenic
Single submitter
Classification
Likely pathogenic
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 12 of 13 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 1.9, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- UBE3A
- Protein
- p.Phe802fs
- Coding
- c.2403_2404del
- MANE Select
- NM_130839
- Type
- Microsatellite
- Location
- chr15:25340179 (GRCh38)
- Gene constraint
- LOEUF 0.139 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 81.42 · 25 PDB
- Residue 802
- the hect domain; an α-helix
Similar variants
- UBE3A p.Phe802Leu Uncertain significance ★ ⚠ same residue
- UBE3A p.Ter873= Benign ★★★ same type
- UBE3A p.Asn470fs Pathogenic ★★ same type
- UBE3A p.Asp810fs Pathogenic ★★ same type
- UBE3A p.Leu490_Tyr491insTer Pathogenic ★★ same type
- UBE3A p.Thr123_Tyr124insTer Pathogenic ★★ same type
- UBE3A p.Glu128fs Pathogenic ★ same type
- UBE3A p.Ser658fs 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/ube3a-p-phe802fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown