STAT3 p.Asn401=
c.1203C>T · rs189708970 · VCV759889
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.008%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -9.9 | GERP -3.7 |
| Overall | ||
| CADD | 0.33 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.008%
African / African-American · 6/75,046 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00228%
Overall
0.00204%
33/1,614,224 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.008% | 12,508 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,837 |
| Finnishnot grpmax-eligible | 0.00312% | 32,023 |
| East Asian | 0.00223% | 44,890 |
| South Asian | 0.0022% | 45,545 |
| Admixed American | 0.00167% | 60,024 |
| European (non-Finnish) | 0.00153% | 65,558 |
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
- STAT3
- Protein
- p.Asn401=
- Coding
- c.1203C>T
- MANE Select
- NM_139276
- dbSNP
- rs189708970
- Type
- single nucleotide variant
- Location
- chr17:42329584 (GRCh38)
- Gene constraint
- LOEUF 0.109 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 85.80 · 6 PDB
- Residue 401
- a turn
Similar variants
- STAT3 p.Asn401Ser Uncertain significance ★ ⚠ same residue
- STAT3 p.Arg152Trp Pathogenic ★★ ⚠ same type
- STAT3 p.Arg278Cys Likely pathogenic ★★ same type
- STAT3 p.Arg335Trp Pathogenic/Likely pathogenic ★★ same type
- STAT3 p.Arg382Gln Pathogenic ★★ same type
- STAT3 p.Arg382Trp Pathogenic ★★ same type
- STAT3 p.Arg423Gln Pathogenic ★★ ⚠ same type
- STAT3 p.Asn466Ser 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/stat3-p-asn401 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown