CD40 p.Pro43=
c.129A>G · rs2085325980 · VCV1525308
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.32 | donor loss · deltas |
|---|---|---|
| Pangolin | Δ0.42 | loss · gain 0.01 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 2 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 17.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/74,926 alleles
Overall
0.000657%
1/152,198 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
- CD40
- Protein
- p.Pro43=
- Coding
- c.129A>G
- MANE Select
- NM_001250
- dbSNP
- rs2085325980
- Type
- single nucleotide variant
- Location
- chr20:46121897 (GRCh38)
- Gene constraint
- LOEUF 0.677 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 81.10 · 14 PDB
- Residue 43
- a disulfide bond
Similar variants
- CD40 c.256+5G>A Uncertain significance ★★ same type
- CD40 c.*178G>A Uncertain significance ★★ same type
- CD40 c.*547A>T Uncertain significance ★★ same type
- CD40 p.Ala25Ser Uncertain significance ★★ ⚠ same type
- CD40 p.Arg123His Uncertain significance ★★ ⚠ same type
- CD40 p.Asn180Lys Uncertain significance ★★ ⚠ same type
- CD40 p.Glu159Lys Uncertain significance ★★ ⚠ same type
- CD40 p.Ile204Val 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/cd40-p-pro43 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown