ITGA3 p.Leu410=
c.1230T>C · rs2285524 · VCV1271172
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 42.4%, 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 -0.041 | GERP -3.9, phastCons 0.001 |
| Overall | ||
| CADD | 2.666 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
42.4%
African / African-American · 31,718/74,882 alleles
Filtering AF
42%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 41.8%
Overall
15.7%
253,991/1,612,682 alleles · common
exomes 217,757/1,460,628 · genomes 36,234/152,054 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 42.4% | 2 |
| Admixed American | 34.8% | 3 |
| East Asian | 34.1% | 3 |
| South Asian | 27.6% | 4 |
| Remaining individualsnot grpmax-eligible | 17.3% | 6 |
| Middle Eastern | 14.4% | 7 |
| Finnishnot grpmax-eligible | 13.7% | 7 |
| Amishnot grpmax-eligible | 13.6% | 7 |
| Ashkenazi Jewishnot grpmax-eligible | 12.7% | 8 |
| European (non-Finnish) | 11.6% | 9 |
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.Leu410=
- Coding
- c.1230T>C
- MANE Select
- NM_002204
- dbSNP
- rs2285524
- Type
- single nucleotide variant
- Location
- chr17:50073989 (GRCh38)
- Gene constraint
- LOEUF 0.69 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.88
Similar variants
- ITGA3 p.Leu410Phe 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-leu410 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown