STAG1 p.Pro596=
c.1788A>G · rs2087997652 · VCV2087784
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00111%, sas)
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 0.63 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 12.13 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00111%
South Asian · 1/89,754 alleles
Overall
0.000124%
2/1,609,392 alleles · very rare
exomes 1/1,457,198 · genomes 1/152,194 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00111% | 89,754 |
| European (non-Finnish) | 8.48e-05% | 1,178,971 |
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
- STAG1
- Protein
- p.Pro596=
- Coding
- c.1788A>G
- MANE Select
- NM_005862
- dbSNP
- rs2087997652
- Type
- single nucleotide variant
- Location
- chr3:136422813 (GRCh38)
- Gene constraint
- LOEUF 0.159 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 79.00 · 20 PDB
- Residue 596
- an α-helix
Similar variants
- STAG1 c.1026+2T>C Likely pathogenic ★★ same type
- STAG1 p.Arg140Ter Pathogenic/Likely pathogenic ★★ same type
- STAG1 p.Arg216Gly Pathogenic/Likely pathogenic ★★ same type
- STAG1 p.Arg373Gln Pathogenic/Likely pathogenic ★★ same type
- STAG1 p.Arg373Ter Pathogenic/Likely pathogenic ★★ same type
- STAG1 p.Arg377Cys Pathogenic/Likely pathogenic ★★ same type
- STAG1 p.Arg395Ter Likely pathogenic ★★ same type
- STAG1 p.Arg971Ter Pathogenic/Likely pathogenic ★★ 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/stag1-p-pro596 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown