STAT5B p.Gly263=
c.789G>A · rs753400820 · VCV747598
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.169%, eas)
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 · C>A here scores Δ0.45 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.054 | GERP -3.7, phastCons 0.93 |
| Overall | ||
| CADD | 9.791 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.169%
East Asian · 68/40,320 alleles
Filtering AF
0.136%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.125%
Overall
0.00472%
70/1,484,294 alleles · rare
exomes 57/1,333,854 · genomes 13/150,440 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.169% | 593 |
| Remaining individualsnot grpmax-eligible | 0.00349% | 28,646 |
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
- STAT5B
- Protein
- p.Gly263=
- Coding
- c.789G>A
- MANE Select
- NM_012448
- dbSNP
- rs753400820
- Type
- single nucleotide variant
- Location
- chr17:42219356 (GRCh38)
- Gene constraint
- LOEUF 0.277 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 85.90 · 2 PDB
- Residue 263
- the 'required for interaction with nmi' region; a turn
Similar variants
- STAT5B p.Gly263Arg Uncertain significance ★★ ⚠ same residue
- STAT5B c.1906+1G>A Likely pathogenic ★★ same type
- STAT5B p.Ala20Glu Uncertain significance ★★ ⚠ same type
- STAT5B p.Ala20Val Uncertain significance ★★ ⚠ same type
- STAT5B p.Ala213Gly Uncertain significance ★★ ⚠ same type
- STAT5B p.Ala213Ser Uncertain significance ★★ ⚠ same type
- STAT5B p.Ala723Thr Uncertain significance ★★ ⚠ same type
- STAT5B p.Ala785Thr 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/stat5b-p-gly263 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown