CD3E p.Leu58fs
c.173del · VCV3340358
Pathogenic
Multiple submitters
Classification
Pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
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 |
|---|---|---|
| NMD | predicted | premature termination codon in exon 6 of 9 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -5.4 | GERP -2.8 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CD3E
- Protein
- p.Leu58fs
- Coding
- c.173del
- MANE Select
- NM_000733
- Type
- Deletion
- Location
- chr11:118312687 (GRCh38)
- Gene constraint
- LOEUF 0.659 · pLI 0.47 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 73.56 · 44 PDB
- Residue 58
- a disulfide bond; a β-strand; the ig-like domain
Similar variants
- CD3E p.Gly143fs Pathogenic ★ same type
- CD3E p.Ser88fs Pathogenic ★ same type
- CD3E c.567+65_567+66del Uncertain significance ★ same type
- CD3E c.70+4del Uncertain significance ★ same type
- CD3E p.Gly68_Gly76del Uncertain significance ★ same type
- CD3E p.Lys177fs Uncertain significance ★ same type
- CD3E c.353-5del Benign ★ same type
- CD3E c.50-10del Likely benign ★ 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/cd3e-p-leu58fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown