ITGA3 p.Thr837=
c.2511C>T · rs143488590 · VCV2188066
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0761%, 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 -2.3 | GERP -3.9 |
| Overall | ||
| CADD | 6.014 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0761%
African / African-American · 57/74,880 alleles
Filtering AF
0.0603%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0546%
Overall
0.00824%
133/1,613,880 alleles · ultra-rare
exomes 93/1,461,792 · genomes 40/152,088 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0761% | 1,314 |
| Middle Eastern | 0.0493% | 2,028 |
| Admixed American | 0.0183% | 5,454 |
| Finnishnot grpmax-eligible | 0.0141% | 7,114 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,414 |
| East Asian | 0.00668% | 14,960 |
| European (non-Finnish) | 0.00364% | 27,440 |
| South Asian | 0.0011% | 91,084 |
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.Thr837=
- Coding
- c.2511C>T
- MANE Select
- NM_002204
- dbSNP
- rs143488590
- Type
- single nucleotide variant
- Location
- chr17:50079186 (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-thr837 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown