STAG2 p.Phe647=
c.1941C>T · rs2148326855 · VCV2898412
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000224%, nfe)
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 2.2 | GERP -2.5, phastCons 1 |
| Overall | ||
| CADD | 11.49 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000224%
European (non-Finnish) · 2/893,650 alleles
Filtering AF
3.7e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.4e-05%
Overall
0.000165%
2/1,209,488 alleles · very rare
exomes 2/1,095,983 · genomes 0/113,505 · joint denominator
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.Phe647=
- Coding
- c.1941C>T
- MANE Select
- NM_001042750
- dbSNP
- rs2148326855
- Type
- single nucleotide variant
- Location
- chrX:124063967 (GRCh38)
- Structure
- AlphaFold pLDDT 80.07 · 10 PDB
- Residue 647
- 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-phe647 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown