ITGB2 p.Pro54=
c.162G>A · rs138303556 · VCV340179
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 -9.3 | GERP -4.2 |
| Overall | ||
| CADD | 0.177 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Ashkenazi Jewishnot grpmax-eligible | 0.398% | 251 |
| European (non-Finnish)grpmax | 0.349% | 286 |
| Remaining individualsnot grpmax-eligible | 0.3% | 333 |
| South Asian | 0.187% | 535 |
| Admixed American | 0.126% | 797 |
| African / African-American | 0.0654% | 1,528 |
| East Asian | 0.0537% | 1,861 |
| Middle Eastern | 0.0357% | 2,800 |
| Finnishnot grpmax-eligible | 0.00473% | 21,152 |
Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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
- ITGB2
- Protein
- p.Pro54=
- Coding
- c.162G>A
- MANE Select
- NM_000211
- dbSNP
- rs138303556
- Type
- single nucleotide variant
- Location
- chr21:44907081 (GRCh38)
- Gene constraint
- LOEUF 0.81 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 86.02 · 29 PDB
- Residue 54
- the psi domain; a β-strand
Disease context
leukocyte adhesion deficiency 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Leukocyte adhesion deficiency (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Childhood, Infancy
Similar variants
- ITGB2 p.Pro54Leu Uncertain significance ★★ ⚠ same residue
- ITGB2 c.741+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ITGB2 c.897+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ITGB2 p.Ala239Thr Pathogenic/Likely pathogenic ★★ same condition
- ITGB2 p.Ala270Val Likely pathogenic ★★ same condition
- ITGB2 p.Arg108Ter Pathogenic/Likely pathogenic ★★ same condition
- ITGB2 p.Arg188Ter Pathogenic ★★ same condition
- ITGB2 p.Arg593Cys Pathogenic ★★ same condition
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/itgb2-p-pro54 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown