STAT3 p.Lys631=
c.1893G>A · VCV4786443
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
2
STAT3 gain of function
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 2.7 | GERP -0.91, phastCons 1 |
| Overall | ||
| CADD | 9.901 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- STAT3
- Protein
- p.Lys631=
- Coding
- c.1893G>A
- MANE Select
- NM_139276
- Type
- single nucleotide variant
- Location
- chr17:42322490 (GRCh38)
- Gene constraint
- LOEUF 0.109 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 85.80 · 6 PDB
- Residue 631
- a modified residue (allysine; alternate); a modified residue (n6-acetyllysine; alternate); the sh2 domain; a cross-link site
Similar variants
- STAT3 p.Arg152Trp Pathogenic ★★ ⚠ same condition
- STAT3 p.Arg278Cys Likely pathogenic ★★ same condition
- STAT3 p.Arg335Trp Pathogenic/Likely pathogenic ★★ same condition
- STAT3 p.Arg382Gln Pathogenic ★★ same condition
- STAT3 p.Arg382Trp Pathogenic ★★ same condition
- STAT3 p.Arg423Gln Pathogenic ★★ ⚠ same condition
- STAT3 p.Asn466Ser Pathogenic ★★ ⚠ same condition
- STAT3 p.Asn466Thr 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/stat3-p-lys631 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown