IRF2BP2 p.Pro108=
c.324G>C · rs1049406389 · VCV1591410
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.091%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.018 | GERP -1.2, phastCons 0.84 |
| Overall | ||
| CADD | 11.49 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.091%
East Asian · 28/30,762 alleles
Filtering AF
0.0647%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0558%
Overall
0.00259%
33/1,274,922 alleles · ultra-rare
exomes 17/1,124,190 · genomes 16/150,732 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.091% | 1,099 |
| Admixed American | 0.0043% | 23,240 |
| Remaining individualsnot grpmax-eligible | 0.00425% | 23,533 |
| South Asian | 0.00258% | 38,792 |
| European (non-Finnish) | 9.86e-05% | 1,014,414 |
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
- IRF2BP2
- Protein
- p.Pro108=
- Coding
- c.324G>C
- MANE Select
- NM_182972
- dbSNP
- rs1049406389
- Type
- single nucleotide variant
- Location
- chr1:234609171 (GRCh38)
- Gene constraint
- LOEUF 0.709 · pLI 0.41 (gnomAD)
- Structure
- AlphaFold pLDDT 56.84 · 3 PDB
Similar variants
- IRF2BP2 p.Pro108Leu Uncertain significance ★ ⚠ same residue
- IRF2BP2 p.Ala143Gly Uncertain significance ★★ ⚠ same type
- IRF2BP2 p.Ala209Gly Uncertain significance ★★ ⚠ same type
- IRF2BP2 p.Ala214Thr Uncertain significance ★★ ⚠ same type
- IRF2BP2 p.Ala246Val Uncertain significance ★★ ⚠ same type
- IRF2BP2 p.Ala254Thr Uncertain significance ★★ ⚠ same type
- IRF2BP2 p.Ala276Thr Uncertain significance ★★ ⚠ same type
- IRF2BP2 p.Ala344Val 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/irf2bp2-p-pro108 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown