STAT2 p.Ser187=
c.561T>C · VCV3771694
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000424%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2 | GERP -2.1, phastCons 0.25 |
| Overall | ||
| CADD | 5.874 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000424%
European (non-Finnish) · 5/1,180,002 alleles
Filtering AF
0.000124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9e-05%
Overall
0.00031%
5/1,613,958 alleles · very rare
exomes 4/1,461,880 · genomes 1/152,078 · 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
- STAT2
- Protein
- p.Ser187=
- Coding
- c.561T>C
- MANE Select
- NM_005419
- Type
- single nucleotide variant
- Location
- chr12:56354850 (GRCh38)
- Gene constraint
- LOEUF 0.497 · pLI 0.81 (gnomAD)
- Structure
- AlphaFold pLDDT 78.45 · 6 PDB
- Residue 187
- the 'mediates interaction with usp18' region
Similar variants
- STAT2 p.Arg667Ter Pathogenic/Likely pathogenic ★★ same type
- STAT2 p.Gln274Ter Pathogenic/Likely pathogenic ★★ same type
- STAT2 p.Ala219Thr Uncertain significance ★★ ⚠ same type
- STAT2 p.Ala302Thr Uncertain significance ★★ ⚠ same type
- STAT2 p.Arg300Cys Uncertain significance ★★ ⚠ same type
- STAT2 p.Arg330Gln Uncertain significance ★★ ⚠ same type
- STAT2 p.Arg409His Uncertain significance ★★ ⚠ same type
- STAT2 p.Arg510Gln 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/stat2-p-ser187 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown