Is STAT2 p.Leu269del (c.804GTT[1]) pathogenic?

STAT2 p.Leu269del (c.804GTT[1]) is classified Uncertain significance in STAT2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-14). No gnomAD frequency available for this variant.

How common is STAT2 p.Leu269del (c.804GTT[1]) in the general population?

STAT2 p.Leu269del (c.804GTT[1]) is no gnomAD frequency available for this variant (gnomAD).

STAT2 p.Leu269del

c.804GTT[1] · rs1592478832 · VCV636346

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.96	GERP -1.3, phastCons 0.99

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: STAT2
Protein: p.Leu269del
Coding: c.804GTT[1]
MANE Select: NM_005419
dbSNP: rs1592478832
Type: Microsatellite
Location: chr12:56351424 (GRCh38)
Gene constraint: LOEUF 0.497 · pLI 0.81 (gnomAD)
Structure: AlphaFold pLDDT 78.45 · 6 PDB
Residue 269: the 'mediates interaction with usp18' region; an α-helix

Full STAT2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

STAT2 p.Glu654del Uncertain significance ★ same type
STAT2 p.Leu536del Uncertain significance ★ same type
STAT2 p.Ser506del Uncertain significance ★ same type
STAT2 c.1116-10_1116-8del Likely benign ★ same type
STAT2 c.1257+16_1257+17del Likely benign ★ same type
STAT2 c.2045-20_2045-18del Likely benign ★ same type
STAT2 c.548-26GACT[3] Likely benign ★ 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/stat2-p-leu269del (accessed [today's date]).

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