STAG2 p.Ser689=
c.2067A>C · rs1297053122 · VCV1969451
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00596%, 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 3.4 | GERP -0.92, phastCons 1 |
| Overall | ||
| CADD | 9.407 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00596%
South Asian · 3/50,340 alleles
Filtering AF
0.00158%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000838%
Overall
0.00034%
4/1,176,793 alleles · very rare
exomes 4/1,063,312 · genomes 0/113,481 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00596% | 16,780 |
| European (non-Finnish) | 0.000114% | 878,758 |
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
- STAG2
- Protein
- p.Ser689=
- Coding
- c.2067A>C
- MANE Select
- NM_001042750
- dbSNP
- rs1297053122
- Type
- single nucleotide variant
- Location
- chrX:124065917 (GRCh38)
- Structure
- AlphaFold pLDDT 80.07 · 10 PDB
- Residue 689
- a UniProt-annotated variant site (in hpe13 and mkms; patient cells show decreased protein abundance; increased sister chromatid cohesion); a UniProt-annotated variant site (in mkms); a UniProt-annotated variant site (in hpe13); an α-helix
Similar variants
- STAG2 p.Arg1012Ter Pathogenic ★★ same type
- STAG2 p.Arg1033Ter Pathogenic ★★ same type
- STAG2 c.1018-3T>A Uncertain significance ★★ same type
- STAG2 c.2924+3A>G Uncertain significance ★★ same type
- STAG2 c.2924+5T>A Uncertain significance ★★ same type
- STAG2 c.3784-3T>C Uncertain significance ★★ same type
- STAG2 p.Ala428Gly Uncertain significance ★★ ⚠ same type
- STAG2 p.Ala532Val 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/stag2-p-ser689 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown