ITGB3 p.Ser596fs
c.1788del · VCV4857363
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 11 of 15 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 2.8 | GERP -0.81, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
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
- ITGB3
- Protein
- p.Ser596fs
- Coding
- c.1788del
- MANE Select
- NM_000212
- Type
- Deletion
- Location
- chr17:47299405 (GRCh38)
- Gene constraint
- LOEUF 0.685 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 87.19 · 125 PDB
- Residue 596
- the i-egf 4 domain
Disease context
Glanzmann thrombasthenia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Glanzmann thrombasthenia (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- ITGB3 c.613_614+2del Pathogenic ★★★ same condition
- ITGB3 p.Ala283fs Pathogenic ★★★ same condition
- ITGB3 p.Ala398fs Pathogenic ★★★ same condition
- ITGB3 p.Arg287fs Pathogenic ★★★ same condition
- ITGB3 p.Arg515fs Likely pathogenic ★★★ same condition
- ITGB3 p.Asn201fs Pathogenic ★★★ same condition
- ITGB3 p.Asn597fs Pathogenic ★★★ same condition
- ITGB3 p.Asp296_His300del Likely 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/itgb3-p-ser596fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown