CD40LG p.Ala13=
c.39G>A · rs779460863 · VCV1169681
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.011%, amr)
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 4.3 | GERP -0.11, phastCons 1 |
| Overall | ||
| CADD | 5.006 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.011%
Admixed American · 5/45,638 alleles
Filtering AF
0.00429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00272%
Overall
0.00317%
38/1,200,025 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.011% | 9,128 |
| South Asian | 0.00884% | 11,313 |
| African / African-American | 0.00529% | 18,915 |
| Remaining individualsnot grpmax-eligible | 0.00423% | 23,642 |
| East Asian | 0.00297% | 33,701 |
| European (non-Finnish) | 0.00248% | 40,304 |
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.Ala13=
- Coding
- c.39G>A
- MANE Select
- NM_000074
- dbSNP
- rs779460863
- Type
- single nucleotide variant
- Location
- chrX:136648287 (GRCh38)
- Structure
- AlphaFold pLDDT 82.34 · 8 PDB
Similar variants
- CD40LG p.Ala13Glu Uncertain significance ★ ⚠ same residue
- CD40LG p.Ala13Val Conflicting classifications of pathogenicity ★ ⚠ same residue
- 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
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-ala13 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown