STAT1 p.Val266Ile
c.796G>A · rs41473544 · VCV333285
Computational evidence
| Protein change | ||
| AlphaMissense | 0.0793 | likely benign |
|---|---|---|
| REVEL | 0.287 | benign-leaning |
| SaProt | LLR -5.75 | tolerated |
| ⇒ AlphaMissense, REVEL and SaProt all call this tolerated. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.52 | GERP -3.7, phastCons 0.075 |
| Regional constraint | o/e 0.42 | unconstrained · MANE · 5,939 bp · p 3.1e-13 · regional, not allelic |
| Overall | ||
| CADD | 14.17 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Finnishnot grpmax-eligible | 0.662% | 151 |
| European (non-Finnish)grpmax | 0.365% | 274 |
| Remaining individualsnot grpmax-eligible | 0.235% | 425 |
| Admixed American | 0.103% | 968 |
| South Asian | 0.0681% | 1,469 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0676% | 1,480 |
| African / African-American | 0.0654% | 1,530 |
Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.
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.Val266Ile
- Coding
- c.796G>A
- MANE Select
- NM_007315
- dbSNP
- rs41473544
- Type
- single nucleotide variant
- Location
- chr2:190995209 (GRCh38)
- Gene constraint
- LOEUF 0.271 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 87.78 · 10 PDB
- Residue 266
- an α-helix
Disease context
immunodeficiency 31B — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: autoimmune enteropathy and endocrinopathy - susceptibility to chronic infections syndromeMendelian susceptibility to mycobacterial diseases due to partial STAT1 deficiency
For Susceptibility to viral and mycobacterial infections due to STAT1 deficiency (Orphanet):
- Inheritance
- Autosomal recessive
Similar variants
- STAT1 p.Ala267Val Pathogenic ★★ ⚠ same condition
- STAT1 p.Arg274Gln Pathogenic ★★ ⚠ same condition
- STAT1 p.Arg274Gly Pathogenic/Likely pathogenic ★★ same condition
- STAT1 p.Arg274Trp Pathogenic ★★ same condition
- STAT1 p.Asp171Asn Likely pathogenic ★★ ⚠ same condition
- STAT1 p.Asp292Glu Likely pathogenic ★★ ⚠ same condition
- STAT1 p.Cys324Arg Likely pathogenic ★★ same condition
- STAT1 p.Gln271Pro Pathogenic/Likely 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/stat1-p-val266ile (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown