EDA p.188PGP[2]
c.570_578del · rs973726321 · VCV1710553
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0128%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.27 | GERP -4.5, phastCons 0.23 |
| Overall | ||
| CADD | 19.74 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | (CCAGGACCC)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0128%
East Asian · 4/31,171 alleles
Filtering AF
0.00429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00261%
Overall
0.00357%
39/1,091,940 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0128% | 7,793 |
| European (non-Finnish) | 0.00411% | 24,311 |
| Remaining individualsnot grpmax-eligible | 0.00229% | 43,622 |
| African / African-American | 0.00187% | 53,548 |
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
- EDA
- Protein
- p.188PGP[2]
- Coding
- c.570_578del
- MANE Select
- NM_001399
- dbSNP
- rs973726321
- Type
- Deletion
- Location
- chrX:70027892 (GRCh38)
- Structure
- AlphaFold pLDDT 70.59 · 3 PDB
Similar variants
- EDA p.202_204IPG[1] Pathogenic/Likely pathogenic ★★ same type
- EDA p.217_219PGP[1] Pathogenic ★★ same type
- EDA p.Ala166fs Pathogenic ★★ same type
- EDA p.Asn185_Pro196del Pathogenic ★★ same type
- EDA p.Gly85fs Pathogenic ★★ same type
- EDA p.Phe317fs Pathogenic ★★ same type
- EDA p.Pro199fs Pathogenic ★★ same type
- EDA p.Pro219_Gly230del Pathogenic/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-188pgp-2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown