STAG2 p.Ser22=
c.66T>C · rs201477761 · VCV1622268
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0233%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>A here scores Δ0.32 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.9 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 11.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0233%
Middle Eastern · 1/4,293 alleles
Filtering AF
0.000573%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000418%
Overall
0.00101%
12/1,184,956 alleles · ultra-rare
exomes 10/1,074,516 · genomes 2/110,440 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0233% | 4,293 |
| South Asian | 0.00191% | 52,484 |
| European (non-Finnish) | 0.00113% | 88,180 |
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.Ser22=
- Coding
- c.66T>C
- MANE Select
- NM_001042750
- dbSNP
- rs201477761
- Type
- single nucleotide variant
- Location
- chrX:124025861 (GRCh38)
- Structure
- AlphaFold pLDDT 80.07 · 10 PDB
- Residue 22
- the 'disordered' region
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-ser22 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown