Is STAT2 c.1209+1del pathogenic?

STAT2 c.1209+1del is classified Pathogenic/Likely pathogenic in STAT2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2020-02-28). Absent from gnomAD; Associated with STAT2-related disorder.

What condition is associated with STAT2 c.1209+1del?

STAT2 c.1209+1del is associated with STAT2-related disorder, primary immunodeficiency with post-measles-mumps-rubella vaccine viral infection (ClinVar).

How common is STAT2 c.1209+1del in the general population?

STAT2 c.1209+1del is absent from gnomAD (gnomAD).

STAT2 c.1209+1del

rs1592475699 · VCV663294

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

canonical splice-site (±1/±2)

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

STAT2-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	canonical splice-site (±1/±2)	predicted loss-of-function
Splicing
Splice region	donor +1	canonical splice dinucleotide (donor +1) · inside the BP7-excluded zone
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.6	GERP 1.4, phastCons 1
Non-coding constraint	Z 1.91	1 kb window · o/e 0.85 · regional · uncalibrated

Predicted loss-of-function is descriptive, not an applied PVS1 code.

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
Coding: c.1209+1del
MANE Select: NM_005419
dbSNP: rs1592475699
Type: Deletion
Location: chr12:56350096 (GRCh38)
Gene constraint: LOEUF 0.497 · pLI 0.81 (gnomAD)
Structure: AlphaFold pLDDT 78.45 · 6 PDB

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

Disease context

STAT2-related disorder

Also linked: primary immunodeficiency with post-measles-mumps-rubella vaccine viral infection

Similar variants

STAT2 p.Gln527fs Pathogenic ★ same condition
STAT2 p.Glu756fs Pathogenic ★ same condition
STAT2 p.Gly609fs Pathogenic ★ same condition
STAT2 p.Leu599fs Pathogenic ★ same condition
STAT2 p.Leu733fs Pathogenic ★ same condition
STAT2 p.Phe553fs Pathogenic ★ same condition
STAT2 p.Thr260fs Pathogenic ★ same condition
STAT2 c.942-15_942-2del Uncertain significance ★ 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/stat2-c-1209-plus-1del (accessed [today's date]).

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