EDA p.Gln247Ter
c.739C>T · rs2520337597 · VCV3252812
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
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 | predicted | premature termination codon in exon 5 of 8 |
| Splicing | ||
| SpliceAI | Δ0.71 | donor loss · deltas |
| Pangolin | Δ0.49 | loss · gain 0.04 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 4.5, phastCons 1 |
| Overall | ||
| CADD | 46.0 | 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.Gln247Ter
- Coding
- c.739C>T
- MANE Select
- NM_001399
- dbSNP
- rs2520337597
- Type
- single nucleotide variant
- Location
- chrX:70029536 (GRCh38)
- Structure
- AlphaFold pLDDT 70.59 · 3 PDB
Similar variants
- EDA p.Gln247His Uncertain significance ★★ ⚠ same residue
- EDA p.Gln247= Pathogenic ★ same residue
- EDA p.Gln247Arg Uncertain significance ★ ⚠ 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
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-gln247ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown