Is STAT1 p.Glu587fs (c.1760_1761del) pathogenic?

STAT1 p.Glu587fs (c.17601761del) is classified Likely pathogenic in STAT1 (ClinVar, Single submitter, 2 submitters; last evaluated 2024-09-22). No gnomAD frequency available for this variant; Associated with immunodeficiency 31B.

What condition is associated with STAT1 p.Glu587fs (c.1760_1761del)?

STAT1 p.Glu587fs (c.1760_1761del) is associated with immunodeficiency 31B (ClinVar).

How common is STAT1 p.Glu587fs (c.1760_1761del) in the general population?

STAT1 p.Glu587fs (c.1760_1761del) is no gnomAD frequency available for this variant (gnomAD).

STAT1 p.Glu587fs

Q: How is Susceptibility to viral and mycobacterial infections due to STAT1 deficiency inherited?

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

c.1760_1761del · rs587776713 · VCV9044

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

immunodeficiency 31B

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 21 of 25
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.8	GERP 1.9, phastCons 1

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: STAT1
Protein: p.Glu587fs
Coding: c.1760_1761del
MANE Select: NM_007315
dbSNP: rs587776713
Type: Microsatellite
Location: chr2:190978968 (GRCh38)
Gene constraint: LOEUF 0.271 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 87.78 · 10 PDB
Residue 587: an α-helix; the sh2 domain

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

Disease context

immunodeficiency 31B — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Susceptibility to viral and mycobacterial infections due to STAT1 deficiency (Orphanet):

Inheritance: Autosomal recessive

Similar variants

STAT1 p.Glu587= Likely benign ★ same residue
STAT1 p.Glu429fs Pathogenic ★ same condition
STAT1 c.1098-19AT[2] Likely benign ★ same condition
STAT1 c.1264-20_1264-18del Likely benign ★ same condition
STAT1 c.463-6_463-3del Likely benign ★ same condition
STAT1 p.Ala267Val Pathogenic ★★ ⚠ same condition
STAT1 p.Arg274Gln Pathogenic ★★ ⚠ same condition
STAT1 p.Arg274Gly Pathogenic/Likely 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-glu587fs (accessed [today's date]).

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