ITGAL p.Pro1152=
c.3456C>T · rs11574950 · VCV714699
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1%, afr)
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 -6 | GERP -3.3 |
| Overall | ||
| CADD | 0.119 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1%
African / African-American · 753/75,048 alleles
Filtering AF
0.944%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.92%
Overall
0.0574%
926/1,614,178 alleles · low-frequency
exomes 502/1,461,866 · genomes 424/152,312 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1% | 100 |
| Middle Eastern | 0.132% | 756 |
| Admixed American | 0.07% | 1,429 |
| Remaining individualsnot grpmax-eligible | 0.064% | 1,563 |
| European (non-Finnish) | 0.00661% | 15,129 |
| South Asian | 0.00439% | 22,772 |
| East Asian | 0.00223% | 44,888 |
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
- ITGAL
- Protein
- p.Pro1152=
- Coding
- c.3456C>T
- MANE Select
- NM_002209
- dbSNP
- rs11574950
- Type
- single nucleotide variant
- Location
- chr16:30521608 (GRCh38)
- Gene constraint
- LOEUF 0.595 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.77 · 41 PDB
- Residue 1152
- the 'disordered' region
Similar variants
- ITGAL c.1213+9T>G Benign ★★ same type
- ITGAL p.Ala307= Benign ★★ same type
- ITGAL p.Arg1020His Benign/Likely benign ★★ ⚠ same type
- ITGAL p.Ser891= Benign ★★ same type
- ITGAL p.Ala1045Pro Uncertain significance ★ ⚠ same type
- ITGAL p.Ala1072Thr Uncertain significance ★ ⚠ same type
- ITGAL p.Ala1127Pro Uncertain significance ★ ⚠ same type
- ITGAL p.Ala1149Pro 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/itgal-p-pro1152 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown