ITGA2B p.Cys911=
c.2733C>T · rs868106253 · VCV3047462
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0838%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.54 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.22 | gain · loss 0.04 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 2.4 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 20.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0838%
Middle Eastern · 5/5,968 alleles
Filtering AF
0.033%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0214%
Overall
0.000839%
13/1,548,738 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0838% | 1,194 |
| Remaining individualsnot grpmax-eligible | 0.00167% | 60,052 |
| European (non-Finnish) | 0.00061% | 163,816 |
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.Cys911=
- Coding
- c.2733C>T
- MANE Select
- NM_000419
- dbSNP
- rs868106253
- Type
- single nucleotide variant
- Location
- chr17:44375106 (GRCh38)
- Gene constraint
- LOEUF 0.763 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.00 · 80 PDB
- Residue 911
- a turn; a disulfide bond
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-cys911 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown