ITGA3 p.Pro867=
c.2601A>T · VCV4750546
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00188%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -9.2 | GERP -3.4 |
| Overall | ||
| CADD | 0.098 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00188%
Admixed American · 1/53,176 alleles
Filtering AF
0.000817%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000661%
Overall
0.00108%
17/1,572,322 alleles · very rare
exomes 13/1,420,142 · genomes 4/152,180 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00188% | 53,176 |
| European (non-Finnish) | 0.00138% | 72,474 |
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
- ITGA3
- Protein
- p.Pro867=
- Coding
- c.2601A>T
- MANE Select
- NM_002204
- Type
- single nucleotide variant
- Location
- chr17:50079452 (GRCh38)
- Gene constraint
- LOEUF 0.69 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.88
- Residue 867
- the 'disordered' region
Similar variants
- ITGA3 c.2070+1G>A Pathogenic ★★ same type
- ITGA3 p.Arg274Gln Likely pathogenic ★★ ⚠ same type
- ITGA3 p.Arg875Ter Likely pathogenic ★★ same type
- ITGA3 c.*48G>A Uncertain significance ★★ same type
- ITGA3 c.*96G>A Uncertain significance ★★ same type
- ITGA3 p.Ala1026Val Uncertain significance ★★ ⚠ same type
- ITGA3 p.Ala1035Val Uncertain significance ★★ ⚠ same type
- ITGA3 p.Arg156Trp 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/itga3-p-pro867 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown