ITGA3 p.Phe332=
c.996C>T · rs2269772 · VCV1271410
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 33.9%, afr) — too common for a highly-penetrant pathogenic allele
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 -0.91 | GERP -4, phastCons 0.007 |
| Overall | ||
| CADD | 8.829 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
33.9%
African / African-American · 25,414/74,904 alleles
Filtering AF
33.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 33.4%
Overall
12.1%
194,753/1,613,448 alleles · common
exomes 166,596/1,461,486 · genomes 28,157/151,962 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 33.9% | 3 |
| East Asian | 31.6% | 3 |
| Admixed American | 24.1% | 4 |
| South Asian | 23.5% | 4 |
| Remaining individualsnot grpmax-eligible | 13.4% | 7 |
| Middle Eastern | 11.8% | 8 |
| Ashkenazi Jewishnot grpmax-eligible | 11.5% | 9 |
| Finnishnot grpmax-eligible | 9.71% | 10 |
| European (non-Finnish) | 8.52% | 12 |
| Amishnot grpmax-eligible | 8.13% | 12 |
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.Phe332=
- Coding
- c.996C>T
- MANE Select
- NM_002204
- dbSNP
- rs2269772
- Type
- single nucleotide variant
- Location
- chr17:50072022 (GRCh38)
- Gene constraint
- LOEUF 0.69 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.88
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-phe332 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown