CD40 p.Thr96fs
c.287_297del · VCV3724127
Pathogenic
Single submitter
Classification
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 |
|---|---|---|
| NMD | predicted | premature termination codon in exon 4 of 9 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 9.6 | GERP 1.8, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CD40
- Protein
- p.Thr96fs
- Coding
- c.287_297del
- MANE Select
- NM_001250
- Type
- Deletion
- Location
- chr20:46122638 (GRCh38)
- Gene constraint
- LOEUF 0.677 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 81.10 · 14 PDB
- Residue 96
- a disulfide bond
Similar variants
- CD40 p.Thr96= Likely benign ★ same residue
- CD40 p.Ter278AlaextTer? Likely pathogenic ★★ same type
- CD40 p.Lys29fs Pathogenic ★ same type
- CD40 p.Met1fs Likely pathogenic ★ same type
- CD40 c.257-17_257-14del Likely benign ★ same type
- CD40 c.498-30_498-11del Likely benign ★ same type
- CD40 c.646+17_646+18del Likely benign ★ same type
- CD40 c.647-14_647-3del 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/cd40-p-thr96fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown