EDA p.Glu308Ter
c.922G>T · rs1131691566 · VCV429747
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | escapes | premature termination codon within the last 50 nt of the penultimate exon (7 of 8, 2 nt from its 3' end) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | Δ0.26 | donor gain · deltas |
| Pangolin | Δ0.32 | gain · loss 0.24 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 4.8, phastCons 1 |
| Overall | ||
| CADD | 45.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- EDA
- Protein
- p.Glu308Ter
- Coding
- c.922G>T
- MANE Select
- NM_001399
- dbSNP
- rs1131691566
- Type
- single nucleotide variant
- Location
- chrX:70033526 (GRCh38)
- Structure
- AlphaFold pLDDT 70.59 · 3 PDB
- Residue 308
- the thd domain
Similar variants
- EDA p.Glu308Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
- EDA c.526+2T>C Pathogenic/Likely pathogenic ★★ same type
- EDA c.526+5G>T Likely pathogenic ★★ same type
- EDA c.527-2A>G Pathogenic/Likely pathogenic ★★ same type
- EDA c.706+1G>A Pathogenic/Likely pathogenic ★★ same type
- EDA c.707-13T>G Pathogenic ★★ same type
- EDA c.742-2A>G Pathogenic/Likely pathogenic ★★ same type
- EDA c.924+1G>T Likely pathogenic ★★ 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/eda-p-glu308ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown