Is STAT3 p.Lys658Arg (c.1973A>G) pathogenic?

STAT3 p.Lys658Arg (c.1973A>G) is classified Likely pathogenic in STAT3 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-05-21). AlphaMissense: likely benign (0.1799); Very rare (popmax 8.47e-05%, nfe); Associated with STAT3-related early-onset multisystem autoimmune disease.

What condition is associated with STAT3 p.Lys658Arg (c.1973A>G)?

STAT3 p.Lys658Arg (c.1973A>G) is associated with STAT3-related early-onset multisystem autoimmune disease (ClinVar).

How common is STAT3 p.Lys658Arg (c.1973A>G) in the general population?

STAT3 p.Lys658Arg (c.1973A>G) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

What do computational predictors say about STAT3 p.Lys658Arg (c.1973A>G)?

AlphaMissense predicts likely benign (score 0.1799) — an in-silico prediction, not a clinical call.

STAT3 p.Lys658Arg

Q: How is STAT3-related early-onset multisystem autoimmune disease inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

c.1973A>G · rs2081520204 · VCV973671

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1799 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

STAT3-related early-onset multisystem autoimmune disease

Computational evidence

Protein change
AlphaMissense	0.1799	likely benign ⚠ discordant with ClinVar
REVEL	0.68	pathogenic-leaning
SaProt	LLR -8.62	tolerated
⇒ REVEL calls this damaging; AlphaMissense and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	GERP 1.9, phastCons 1
Regional constraint	o/e 0.13	constrained · MANE · 716 bp · p 9e-16 · regional, not allelic
Overall
CADD	31.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,180,036 alleles

Overall 6.19e-05% 1/1,614,234 alleles · very rare exomes 1/1,461,890 · genomes 0/152,344 · 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: STAT3
Protein: p.Lys658Arg
Coding: c.1973A>G
MANE Select: NM_139276
dbSNP: rs2081520204
Type: single nucleotide variant
Location: chr17:42322410 (GRCh38)
Gene constraint: LOEUF 0.109 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 85.80 · 6 PDB
Residue 658: the sh2 domain; a UniProt-annotated variant site (in admio1); a UniProt-annotated variant site (in admio1; uncertain significance)

Full STAT3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

STAT3-related early-onset multisystem autoimmune disease — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For STAT3-related early-onset multisystem autoimmune disease (Orphanet):

Inheritance: Autosomal dominant
Onset: Childhood, Infancy

Similar variants

STAT3 p.Lys658Asn Pathogenic same residue
STAT3 p.Arg152Trp Pathogenic ★★ ⚠ same condition
STAT3 p.Arg382Trp Pathogenic ★★ same condition
STAT3 p.Arg423Gln Pathogenic ★★ ⚠ same condition
STAT3 p.Glu415Lys Pathogenic/Likely pathogenic ★★ same condition
STAT3 p.Gly421Arg Pathogenic/Likely pathogenic ★★ ⚠ same condition
STAT3 p.Pro715Leu Pathogenic/Likely pathogenic ★★ ⚠ same condition
STAT3 p.Thr716Met 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-lys658arg (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown