Is TREX1 p.Ser46fs (c.137dup) pathogenic?

TREX1 p.Ser46fs (c.137dup) is classified Pathogenic/Likely pathogenic in TREX1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-20). No gnomAD frequency available for this variant; Associated with Aicardi-Goutieres syndrome 1.

What condition is associated with TREX1 p.Ser46fs (c.137dup)?

TREX1 p.Ser46fs (c.137dup) is associated with Aicardi-Goutieres syndrome 1, chilblain lupus 1 (ClinVar).

How common is TREX1 p.Ser46fs (c.137dup) in the general population?

TREX1 p.Ser46fs (c.137dup) is no gnomAD frequency available for this variant (gnomAD).

How is Aicardi-Goutières syndrome inherited?

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

TREX1 p.Ser46fs

c.137dup · rs2107255865 · VCV1299626

Pathogenic/Likely pathogenic Single submitter

Classification

Pathogenic/Likely 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

Aicardi-Goutieres syndrome 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 3.4	GERP 1.8, phastCons 0.97

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: TREX1
Protein: p.Ser46fs
Coding: c.137dup
MANE Select: NM_130384 · reported on NM_033629
dbSNP: rs2107255865
Type: Duplication
Location: chr3:48466791 (GRCh38)

Full TREX1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Aicardi-Goutieres syndrome 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: chilblain lupus 1

For Aicardi-Goutières syndrome (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive
Onset: Antenatal, Infancy, Neonatal
Prevalence: 1-5 / 10 000 (Europe)

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/trex1-p-ser46fs (accessed [today's date]).

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