EDA2R p.Pro45=
c.135T>A · rs752010334 · VCV709200
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00492%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.20 | acceptor loss · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.5 | GERP -3.1, phastCons 1 |
| Overall | ||
| CADD | 6.744 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00492%
European (non-Finnish) · 44/894,381 alleles
Filtering AF
0.00373%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00332%
Overall
0.00373%
45/1,208,011 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00492% | 20,327 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,538 |
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
- EDA2R
- Protein
- p.Pro45=
- Coding
- c.135T>A
- MANE Select
- NM_021783
- dbSNP
- rs752010334
- Type
- single nucleotide variant
- Location
- chrX:66605179 (GRCh38)
- Structure
- AlphaFold pLDDT 69.14
- Residue 45
- a disulfide bond
Similar variants
- EDA2R p.Pro45Leu Uncertain significance ★ ⚠ same residue
- EDA2R p.Leu27= Benign ★★ same type
- EDA2R p.Pro112Ser Likely benign ★★ ⚠ same type
- EDA2R p.Tyr8His Benign ★★ same type
- EDA2R p.Ala119Val Uncertain significance ★ ⚠ same type
- EDA2R p.Arg14Gln Uncertain significance ★ ⚠ same type
- EDA2R p.Arg47Cys Uncertain significance ★ ⚠ same type
- EDA2R p.Arg95Cys Uncertain significance ★ ⚠ 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/eda2r-p-pro45 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown