IL23R p.Pro124=
c.372G>A · rs143803981 · VCV735871
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.507%, afr)
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 -0.17 | GERP -4.6, phastCons 0.008 |
| Overall | ||
| CADD | 7.572 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.507%
African / African-American · 380/74,992 alleles
Filtering AF
0.465%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.448%
Overall
0.0333%
538/1,613,818 alleles · rare
exomes 274/1,461,592 · genomes 264/152,226 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.507% | 197 |
| Remaining individualsnot grpmax-eligible | 0.0752% | 1,330 |
| Admixed American | 0.0617% | 1,622 |
| South Asian | 0.0275% | 3,643 |
| East Asian | 0.00446% | 22,434 |
| European (non-Finnish) | 0.00398% | 25,103 |
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
- IL23R
- Protein
- p.Pro124=
- Coding
- c.372G>A
- MANE Select
- NM_144701
- dbSNP
- rs143803981
- Type
- single nucleotide variant
- Location
- chr1:67182840 (GRCh38)
- Gene constraint
- LOEUF 0.739 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.76 · 4 PDB
- Residue 124
- an α-helix
Similar variants
- IL23R p.Pro124Leu Uncertain significance ★★ ⚠ same residue
- IL23R p.Ala531Thr Uncertain significance ★★ ⚠ same type
- IL23R p.Cys115Gly Uncertain significance ★★ ⚠ same type
- IL23R p.Cys558Arg Uncertain significance ★★ ⚠ same type
- IL23R p.Gln465Pro Uncertain significance ★★ ⚠ same type
- IL23R p.Gln564Lys Uncertain significance ★★ ⚠ same type
- IL23R p.Glu169Lys Uncertain significance ★★ ⚠ same type
- IL23R p.Glu205Val 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/il23r-p-pro124 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown