CD40 p.Ile33del
c.95TAA[1] · rs1568905451 · VCV29611
Pathogenic
No assertion criteria
Classification
Pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Conditions
1
hyper-IgM syndrome type 3
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.3 | GERP 0.26 |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- CD40
- Protein
- p.Ile33del
- Coding
- c.95TAA[1]
- MANE Select
- NM_001250
- dbSNP
- rs1568905451
- Type
- Microsatellite
- Location
- chr20:46121863 (GRCh38)
- Gene constraint
- LOEUF 0.677 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 81.10 · 14 PDB
- Residue 33
- a β-strand
Similar variants
- CD40 p.Ter278AlaextTer? Likely pathogenic ★★ same condition
- CD40 c.*178G>A Uncertain significance ★★ same condition
- CD40 c.*547A>T Uncertain significance ★★ same condition
- CD40 c.403+20A>G Benign/Likely benign ★★ same condition
- CD40 c.52-15C>T Benign/Likely benign ★★ same condition
- CD40 c.559+36G>C Benign ★★ same condition
- CD40 c.647-3dup Benign ★★ same condition
- CD40 c.-1T>C Benign/Likely benign ★★ same condition
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/cd40-p-ile33del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown