STAG2 p.Arg560=
c.1680G>A · rs2521797370 · VCV2431611
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
holoprosencephaly 13, X-linked
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 3.3 | GERP 0.37, phastCons 1 |
| Overall | ||
| CADD | 8.654 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- STAG2
- Protein
- p.Arg560=
- Coding
- c.1680G>A
- MANE Select
- NM_001042750
- dbSNP
- rs2521797370
- Type
- single nucleotide variant
- Location
- chrX:124062943 (GRCh38)
- Structure
- AlphaFold pLDDT 80.07 · 10 PDB
- Residue 560
- 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.Arg560Lys Likely benign ★★ same residue
- STAG2 p.Arg560Gly Uncertain significance ★ ⚠ same residue
- STAG2 p.Arg1012Ter Pathogenic ★★ same condition
- STAG2 p.Met1180Val Uncertain significance ★★ same condition
- STAG2 c.1417-39A>C Benign ★★ same condition
- STAG2 c.45-11T>C Benign/Likely benign ★★ same condition
- STAG2 p.Phe367= Benign/Likely benign ★★ same condition
- STAG2 c.2096+2T>A Pathogenic ★ same condition
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-arg560 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown