CD40LG p.Ser12fs
c.34dup · VCV4733951
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
hyper-IgM syndrome type 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 1 of 5 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.77 | GERP -3.5, phastCons 0.57 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CD40LG
- Protein
- p.Ser12fs
- Coding
- c.34dup
- MANE Select
- NM_000074
- Type
- Duplication
- Location
- chrX:136648281 (GRCh38)
- Structure
- AlphaFold pLDDT 82.34 · 8 PDB
Similar variants
- CD40LG p.Gly199fs Pathogenic ★ same condition
- CD40LG p.Ser128fs Pathogenic ★ same condition
- CD40LG p.Tyr170fs Pathogenic ★ same condition
- CD40LG p.Val163Ter Uncertain significance ★ same condition
- CD40LG c.346+5_346+11dup Likely benign ★ same condition
- CD40LG p.Val64fs Pathogenic same condition
- CD40LG c.158_161del Pathogenic/Likely pathogenic ★★ same condition
- CD40LG c.346+5G>A 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-ser12fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown