CD40LG p.Ile2=
c.6C>T · rs767236871 · VCV760534
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0814%, sas)
Conditions
1
hyper-IgM syndrome type 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.18 | GERP -1.4, phastCons 0.94 |
| Overall | ||
| CADD | 7.342 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0814%
South Asian · 46/56,484 alleles
Filtering AF
0.0627%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0561%
Overall
0.00442%
53/1,200,358 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0814% | 1,228 |
| African / African-American | 0.00353% | 28,315 |
| Remaining individualsnot grpmax-eligible | 0.00211% | 47,295 |
| European (non-Finnish) | 0.000451% | 221,829 |
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
- CD40LG
- Protein
- p.Ile2=
- Coding
- c.6C>T
- MANE Select
- NM_000074
- dbSNP
- rs767236871
- Type
- single nucleotide variant
- Location
- chrX:136648254 (GRCh38)
- Structure
- AlphaFold pLDDT 82.34 · 8 PDB
Similar variants
- CD40LG c.346+5G>A Pathogenic/Likely pathogenic ★★ same condition
- CD40LG c.347-2A>G Pathogenic ★★ same condition
- CD40LG p.Arg11Ter Pathogenic ★★ same condition
- CD40LG p.Cys218Ter Pathogenic ★★ same condition
- CD40LG p.Gln160Ter Pathogenic ★★ same condition
- CD40LG p.Gln174Ter Pathogenic/Likely pathogenic ★★ same condition
- CD40LG p.Gln220Ter Pathogenic ★★ same condition
- CD40LG p.Gln90Ter Pathogenic ★★ 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/cd40lg-p-ile2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown