STAT1 p.Asp59=
c.177C>T · rs1187208513 · VCV747287
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
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 4.3 | GERP -0.24, phastCons 1 |
| Overall | ||
| CADD | 14.47 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,008 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000186%
3/1,613,956 alleles · very rare
exomes 2/1,461,784 · genomes 1/152,172 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 60,008 |
| European (non-Finnish) | 0.000169% | 589,981 |
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
- STAT1
- Protein
- p.Asp59=
- Coding
- c.177C>T
- MANE Select
- NM_007315
- dbSNP
- rs1187208513
- Type
- single nucleotide variant
- Location
- chr2:191009059 (GRCh38)
- Gene constraint
- LOEUF 0.271 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 87.78 · 10 PDB
- Residue 59
- an α-helix
Similar variants
- STAT1 p.Ala267Val Pathogenic ★★ ⚠ same type
- STAT1 p.Arg274Gln Pathogenic ★★ ⚠ same type
- STAT1 p.Arg274Gly Pathogenic/Likely pathogenic ★★ same type
- STAT1 p.Arg274Trp Pathogenic ★★ same type
- STAT1 p.Asp171Asn Likely pathogenic ★★ ⚠ same type
- STAT1 p.Asp292Glu Likely pathogenic ★★ ⚠ same type
- STAT1 p.Cys324Arg Likely pathogenic ★★ same type
- STAT1 p.Gln271Pro Pathogenic/Likely pathogenic ★★ ⚠ 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/stat1-p-asp59 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown