STAT1 p.Asp575=
c.1725T>C · VCV4684630
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000934%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.21 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.2 | GERP -1.8, phastCons 0.2 |
| Overall | ||
| CADD | 9.162 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000934%
European (non-Finnish) · 11/1,177,984 alleles
Filtering AF
0.000501%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000366%
Overall
0.000682%
11/1,611,804 alleles · very rare
exomes 10/1,459,618 · genomes 1/152,186 · 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
- STAT1
- Protein
- p.Asp575=
- Coding
- c.1725T>C
- MANE Select
- NM_007315
- Type
- single nucleotide variant
- Location
- chr2:190979774 (GRCh38)
- Gene constraint
- LOEUF 0.271 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 87.78 · 10 PDB
- Residue 575
- an α-helix; the sh2 domain
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-asp575 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown