Is STAT1 p.Arg274Trp (c.820C>T) pathogenic?

STAT1 p.Arg274Trp (c.820C>T) is classified Pathogenic in STAT1 (ClinVar, Multiple submitters, 10 submitters; last evaluated 2026-08-11). AlphaMissense: ambiguous (0.5268); Absent from gnomAD v4.1; Associated with STAT1-related disorder.

How common is STAT1 p.Arg274Trp (c.820C>T) in the general population?

STAT1 p.Arg274Trp (c.820C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about STAT1 p.Arg274Trp (c.820C>T)?

AlphaMissense predicts ambiguous (score 0.5268) — an in-silico prediction, not a clinical call.

STAT1 p.Arg274Trp

Q: What condition is associated with STAT1 p.Arg274Trp (c.820C>T)?

STAT1 p.Arg274Trp (c.820C>T) is associated with STAT1-related disorder, immunodeficiency 31B, autoimmune enteropathy and endocrinopathy - susceptibility to chronic infections syndrome (ClinVar).

c.820C>T · rs387906758 · VCV30083

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 10 submitters

AlphaMissense

ambiguous

0.5268 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

REVEL, SaProt · AlphaMissense indeterminate

Conditions

STAT1-related disorder

Computational evidence

Protein change
AlphaMissense	0.5268	ambiguous
REVEL	0.854	moderately pathogenic-leaning
SaProt	LLR -10.35	damaging
⇒ REVEL and SaProt both call this damaging; AlphaMissense is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.9, phastCons 1
Regional constraint	o/e 0.00	constrained · MANE · 46 bp · p 2.8e-05 · regional, not allelic
Overall
CADD	34.0	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

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: STAT1
Protein: p.Arg274Trp
Coding: c.820C>T
MANE Select: NM_007315
dbSNP: rs387906758
Type: single nucleotide variant
Location: chr2:190995185 (GRCh38)
Gene constraint: LOEUF 0.271 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 87.78 · 10 PDB
Residue 274: an α-helix; a UniProt-annotated variant site (in imd31c; gain of function; increases stat1 phosphorylation due to impaired nuclear dephosphorylation; increases transactivation activity in response to ifng); a UniProt-annotated variant site (in imd31c; gain of function; increases phosphorylation in response to ifng, ifna and il27 due to a loss of dephosphorylation)

Full STAT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

STAT1-related disorder

Also linked: immunodeficiency 31B autoimmune enteropathy and endocrinopathy - susceptibility to chronic infections syndrome Mendelian susceptibility to mycobacterial diseases due to partial STAT1 deficiency

Similar variants

STAT1 p.Arg274Gln Pathogenic ★★ ⚠ same residue
STAT1 p.Arg274Gly Pathogenic/Likely pathogenic ★★ same residue
STAT1 p.Ala267Val 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
STAT1 p.Phe172Leu 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-arg274trp (accessed [today's date]).

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