ITGA3 c.*33G>A
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.185%, afr)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.372 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 8.5 | GERP 1.1, phastCons 1 |
| Non-coding constraint | Z 1.54 | 1 kb window · o/e 0.90 · regional · uncalibrated |
| Overall | ||
| CADD | 19.19 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.185%
African / African-American · 139/74,994 alleles
Filtering AF
0.16%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.151%
Overall
0.0098%
158/1,612,266 alleles · rare
exomes 78/1,460,038 · genomes 80/152,228 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.185% | 540 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,677 |
| Admixed American | 0.0133% | 7,497 |
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
- Coding
- c.*33G>A
- MANE Select
- NM_002204
- dbSNP
- rs78434961
- Type
- single nucleotide variant
- Location
- chr17:50089111 (GRCh38)
- Gene constraint
- LOEUF 0.69 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.88
Similar variants
- ITGA3 p.Arg293Trp Uncertain significance ★★ ⚠ same condition
- ITGA3 p.Arg524His Uncertain significance ★★ ⚠ same condition
- ITGA3 p.Arg525Trp Uncertain significance ★★ ⚠ same condition
- ITGA3 p.Arg589Pro Uncertain significance ★★ ⚠ same condition
- ITGA3 p.Arg932Gln Uncertain significance ★★ ⚠ same condition
- ITGA3 p.Glu668Asp Uncertain significance ★★ same condition
- ITGA3 p.Gly533Ser Uncertain significance ★★ ⚠ same condition
- ITGA3 p.Leu410Phe Uncertain significance ★★ ⚠ 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/itga3-c-star-33g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown