IL2RA p.Pro29=
c.87A>T · VCV4906500
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6.9 | GERP -3.5 |
| Overall | ||
| CADD | 0.114 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,024 alleles
Overall
6.2e-05%
1/1,613,398 alleles · very rare
exomes 1/1,461,070 · genomes 0/152,328 · joint denominator
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
- IL2RA
- Protein
- p.Pro29=
- Coding
- c.87A>T
- MANE Select
- NM_000417
- Type
- single nucleotide variant
- Location
- chr10:6026003 (GRCh38)
- Gene constraint
- LOEUF 0.906 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 72.72 · 10 PDB
- Residue 29
- an α-helix; the sushi 1 domain
Similar variants
- IL2RA p.Pro29Leu Uncertain significance ★ same residue
- IL2RA p.Gln101Ter Pathogenic ★★ same type
- IL2RA c.655+4C>T Uncertain significance ★★ same type
- IL2RA c.*1026G>T Uncertain significance ★★ same type
- IL2RA p.Arg206Cys Uncertain significance ★★ ⚠ same type
- IL2RA p.Arg206His Uncertain significance ★★ ⚠ same type
- IL2RA p.Arg263Trp Uncertain significance ★★ ⚠ same type
- IL2RA p.Arg56His 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/il2ra-p-pro29 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown