Is STING1 p.Phe153Ile (c.457T>A) pathogenic?

STING1 p.Phe153Ile (c.457T>A) is classified Likely pathogenic in STING1 (ClinVar, Single submitter, 2 submitters; last evaluated 2024-02-18). AlphaMissense: likely benign (0.201); Absent from gnomAD v4.1; Associated with STING-associated vasculopathy with onset in infancy.

What condition is associated with STING1 p.Phe153Ile (c.457T>A)?

STING1 p.Phe153Ile (c.457T>A) is associated with STING-associated vasculopathy with onset in infancy (ClinVar).

How common is STING1 p.Phe153Ile (c.457T>A) in the general population?

STING1 p.Phe153Ile (c.457T>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about STING1 p.Phe153Ile (c.457T>A)?

AlphaMissense predicts likely benign (score 0.201) — an in-silico prediction, not a clinical call.

STING1 p.Phe153Ile

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.457T>A · rs2152094234 · VCV1299706

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.201 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

STING-associated vasculopathy with onset in infancy

Computational evidence

Protein change
AlphaMissense	0.201	likely benign ⚠ discordant with ClinVar
REVEL	0.065	moderately benign-leaning
SaProt	LLR -0.84	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.6	GERP -0.82, phastCons 0.98
Regional constraint	o/e 0.77	unconstrained · MANE · 5,440 bp · p 3e-07 · regional, not allelic
Overall
CADD	14.88	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: STING1
Protein: p.Phe153Ile
Coding: c.457T>A
MANE Select: NM_198282
dbSNP: rs2152094234
Type: single nucleotide variant
Location: chr5:139480853 (GRCh38)
Gene constraint: LOEUF 0.846 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.13 · 125 PDB
Residue 153: the 'mediates interaction with zdhhc1 and zdhhc11' region; the 'cyclic dinucleotide-binding domain (cbd)' region

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-phe153ile (accessed [today's date]).

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