ITGA2B p.Pro289=
c.867C>G · rs1047920032 · VCV435531
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00017%, nfe)
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 -1.5 | GERP -3 |
| Overall | ||
| CADD | 2.098 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,179,940 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,613,640 alleles · very rare
exomes 2/1,461,402 · genomes 0/152,238 · 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
- ITGA2B
- Protein
- p.Pro289=
- Coding
- c.867C>G
- MANE Select
- NM_000419
- dbSNP
- rs1047920032
- Type
- single nucleotide variant
- Location
- chr17:44384335 (GRCh38)
- Gene constraint
- LOEUF 0.763 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.00 · 80 PDB
Similar variants
- ITGA2B c.1210+105A>G Likely pathogenic ★★★ same type
- ITGA2B c.1210+5G>A Likely pathogenic ★★★ same type
- ITGA2B c.1211-1G>C Likely pathogenic ★★★ same type
- ITGA2B c.1544+1G>A Pathogenic ★★★ same type
- ITGA2B c.1545-1G>A Pathogenic ★★★ same type
- ITGA2B c.1600+1G>A Pathogenic ★★★ same type
- ITGA2B c.1752+2T>C Pathogenic ★★★ same type
- ITGA2B c.1753-1G>A 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/itga2b-p-pro289 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown