Is STAT2 p.Thr260fs (c.778del) pathogenic?

STAT2 p.Thr260fs (c.778del) is classified Pathogenic in STAT2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-23). Absent from gnomAD; Associated with primary immunodeficiency with post-measles-mumps-rubella vaccine viral infection.

How common is STAT2 p.Thr260fs (c.778del) in the general population?

STAT2 p.Thr260fs (c.778del) is absent from gnomAD (gnomAD).

STAT2 p.Thr260fs

Q: What condition is associated with STAT2 p.Thr260fs (c.778del)?

STAT2 p.Thr260fs (c.778del) is associated with primary immunodeficiency with post-measles-mumps-rubella vaccine viral infection (ClinVar).

Q: How is Primary immunodeficiency with post-measles-mumps-rubella vaccine viral infection inherited?

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

c.778del · rs2547264815 · VCV2798041

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

primary immunodeficiency with post-measles-mumps-rubella vaccine viral infection

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 8 of 24
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.2	GERP -0.69, phastCons 0.87

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
Protein: p.Thr260fs
Coding: c.778del
MANE Select: NM_005419
dbSNP: rs2547264815
Type: Deletion
Location: chr12:56354470 (GRCh38)
Gene constraint: LOEUF 0.497 · pLI 0.81 (gnomAD)
Structure: AlphaFold pLDDT 78.45 · 6 PDB
Residue 260: the 'mediates interaction with usp18' region; an α-helix

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

Disease context

primary immunodeficiency with post-measles-mumps-rubella vaccine viral infection — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Primary immunodeficiency with post-measles-mumps-rubella vaccine viral infection (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy

Similar variants

STAT2 p.Thr260= Likely benign ★ same residue
STAT2 c.1209+1del Pathogenic/Likely pathogenic ★★ same condition
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

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-thr260fs (accessed [today's date]).

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