Is STING1 p.Pro92= (c.276C>A) pathogenic?

STING1 p.Pro92= (c.276C>A) is classified Likely benign in STING1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-16). Very rare (popmax 0.000424%, nfe); Associated with STING-associated vasculopathy with onset in infancy.

What condition is associated with STING1 p.Pro92= (c.276C>A)?

STING1 p.Pro92= (c.276C>A) is associated with STING-associated vasculopathy with onset in infancy (ClinVar).

How common is STING1 p.Pro92= (c.276C>A) in the general population?

STING1 p.Pro92= (c.276C>A) is very rare (popmax 0.000424%, nfe) (gnomAD).

STING1 p.Pro92=

Q: How is STING-associated vasculopathy with onset in infancy inherited?

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

c.276C>A · rs544170120 · VCV2977709

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000424%, nfe)

Conditions

STING-associated vasculopathy with onset in infancy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.055	GERP -2.8, phastCons 0.001
Overall
CADD	2.228	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000424% European (non-Finnish) · 5/1,179,106 alleles

Filtering AF 0.000124% ClinGen BA1/BS1 input FAF95, joint · FAF99 9e-05%

Overall 0.000342% 5/1,459,856 alleles · very rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: STING1
Protein: p.Pro92=
Coding: c.276C>A
MANE Select: NM_198282
dbSNP: rs544170120
Type: single nucleotide variant
Location: chr5:139481294 (GRCh38)
Gene constraint: LOEUF 0.846 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.13 · 125 PDB
Residue 92: the 'mediates interaction with zdhhc1 and zdhhc11' region; an α-helix

Full STING1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

STING-associated vasculopathy with onset in infancy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For STING-associated vasculopathy with onset in infancy (Orphanet):

Inheritance: Autosomal dominant
Onset: Infancy
Prevalence: <1 / 1 000 000 (Worldwide)

Similar variants

STING1 p.Arg281Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
STING1 p.Arg284Ser Pathogenic ★★ same condition
STING1 p.Val155Met Pathogenic ★★ ⚠ same condition
STING1 c.946+1G>T Uncertain significance ★★ same condition
STING1 p.Ala22Asp Uncertain significance ★★ ⚠ same condition
STING1 p.Ala233Thr Uncertain significance ★★ same condition
STING1 p.Ala254Val Uncertain significance ★★ ⚠ same condition
STING1 p.Ala262Thr 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/sting1-p-pro92 (accessed [today's date]).

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