ITGA3 p.Pro1041=
c.3123G>A · rs369707809 · VCV1666093
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0268%, afr)
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 -0.64 | GERP -3.3, phastCons 0.001 |
| Overall | ||
| CADD | 11.44 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0268%
African / African-American · 20/74,608 alleles
Filtering AF
0.0178%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0148%
Overall
0.00498%
79/1,587,788 alleles · ultra-rare
exomes 66/1,435,462 · genomes 13/152,326 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0268% | 3,730 |
| Middle Eastern | 0.0166% | 6,028 |
| Admixed American | 0.0161% | 6,213 |
| Remaining individualsnot grpmax-eligible | 0.013% | 7,691 |
| East Asian | 0.00687% | 14,553 |
| European (non-Finnish) | 0.00308% | 32,426 |
| Finnishnot grpmax-eligible | 0.00163% | 61,352 |
| South Asian | 0.00114% | 87,358 |
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.Pro1041=
- Coding
- c.3123G>A
- MANE Select
- NM_002204
- dbSNP
- rs369707809
- Type
- single nucleotide variant
- Location
- chr17:50088302 (GRCh38)
- Gene constraint
- LOEUF 0.69 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.88
Similar variants
- ITGA3 p.Pro1041Gln Uncertain significance ★ ⚠ same residue
- 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
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-pro1041 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown