CD3E p.Glu189=
c.567G>A · VCV4689608
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.69 | donor loss · deltas |
|---|---|---|
| Pangolin | Δ0.73 | loss · gain 0.01 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 22.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,804 alleles
Overall
6.84e-05%
1/1,461,574 alleles · very rare
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
- CD3E
- Protein
- p.Glu189=
- Coding
- c.567G>A
- MANE Select
- NM_000733
- Type
- single nucleotide variant
- Location
- chr11:118314494 (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 189
- the itam domain; the 'disordered' region; the 'numb-binding region' region
Similar variants
- CD3E c.103+1G>A Likely pathogenic ★★ same type
- CD3E c.49+1G>C Pathogenic ★★ same type
- CD3E p.Tyr96Ter Pathogenic/Likely pathogenic ★★ same type
- CD3E c.520+5G>A Uncertain significance ★★ same type
- CD3E p.Arg192Gln Uncertain significance ★★ ⚠ same type
- CD3E p.Arg206His Uncertain significance ★★ ⚠ same type
- CD3E p.Asn25Asp Uncertain significance ★★ ⚠ same type
- CD3E p.Asn74Thr Uncertain significance ★★ ⚠ 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-glu189 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown