ITGA3 p.Thr972=
c.2916G>A · VCV3676743
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00404%, afr)
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 -1.6 | GERP -3.8 |
| Overall | ||
| CADD | 7.318 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00404%
African / African-American · 3/74,182 alleles
Filtering AF
0.00107%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000498%
Overall
0.000509%
8/1,571,840 alleles · very rare
exomes 8/1,419,544 · genomes 0/152,296 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00404% | 24,727 |
| European (non-Finnish) | 0.000433% | 231,191 |
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.Thr972=
- Coding
- c.2916G>A
- MANE Select
- NM_002204
- Type
- single nucleotide variant
- Location
- chr17:50081405 (GRCh38)
- Gene constraint
- LOEUF 0.69 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.88
Similar variants
- ITGA3 p.Thr972Met 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-thr972 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown